Labels and headers should display the correct english localization

[Gregory Vincic]

In some places there is no localized value. Enter these values in the client/servlet/src/locale/en/dictionary.

[olle]

Ticket accepted.

[olle]

Changeset related to localization added 2007-10-11 21:14:35 by gregory:

(In ​[2106]). Moved localization to GUIConverter and HTMLFactory. All localization inside actions may now be removed and replaced with localized keywords. To help with the identification of missing keywords. A logger has been added to log4j.properties.in which warns if a keyword is missing in the dictionary.

[olle]

Changeset related to localization added 2007-10-11 21:53:28 by gregory:

(In ​[2107]). Refs #285. Removed localization from ViewLeft action.

[olle]

(In [2113]) Refs #287. Refs #285. Removed localization from TableFactory?, i.e. no call is made to a Localizer item. The Localizer instance variable is kept, together with its public setter method void setLocale(Localizer locale), so as not to break the code in other classes calling the latter. When these references are removed, the Localizer variable and method void setLocale(Localizer locale can be removed from TableFactory?.

[Gregory Vincic]

(In [2119]) Refs #287. Improved the warning message when keys are missing translations.

[olle]

(In [2121]) Refs #287. English localization dictionary file locale/en/dictionary in client/servlet/ updated with changed and new entries. Most localized versions consist of changing "CamelCase" keys by inserting a space between component words, e.g. "ExperimentalMass?=Experimental Mass". Exceptions were made for entries where convention dictate otherwise, e.g. "DeltaMass?=Deltamass" or "MicroPlate?=Microplate", and entries containing abbreviations with upper-case letters, e.g. "Md5=MD5" or "RMSError=RMS Error".

1. New entries added.
2. Old entries with initial lower-case letter in the key were

duplicated with initial upper-case letter in the key.

3. Some old entries were updated to be consistent, e.g. abbreviating

index as "Id" instead of "ID".

[Fredrik Levander]

(In [2123]) Refs #287. The path had to be forward slash for resource on windows

[Fredrik Levander]

(In [2124]) Refs #265. Refs #287. Added fields for all functions to gel form. Added new terms to dictionary

[olle]

(In [2127]) Refs #287. English localization dictionary file locale/en/dictionary in client/servlet/ updated with entry "ClearHits?=Clear Hits".

[Fredrik Levander]

(In [2133]) Refs #287. Length of IPG strip

[olle]

(In [2134]) Refs #287. Localization support added for Hits columns "Mw" and "Pi".

1. Class/file gui/table/TableFactory.java in client/servlet/ updated

in private method void initializeColumnNameToUse() to use column key "TheoreticalMolecularMassDa?" for "Mw" and "TheoreticalPi?" for "Pi" for the Hit.class. This avoids problems if the same short notations "Mw" or "Pi" should be used for other quantities in other classes.

2. English localization dictionary file locale/en/dictionary in

client/servlet/ updated with entries "TheoreticalMolecularMassDa?=Theoretical molecular mass (Da)" and "TheoreticalPi?=Theoretical pI".

[olle]

(In [2144]) Refs #291. Refs #287. Names of some getter and setter methods updated with suffix indicating the unit the value is expressed in. Below the getter methods are listed:

1. GelElectrophoresis?:

getMassStartInKiloDaltons(), getMassEndInKiloDaltons(), getSizeXInCentiMeters(), getSizeYInCentiMeters().

2. Hit:

getMwInDaltons().

3. IPG:

getLengthInCentiMeters().

[olle]

(In [2146]) Refs #291. Refs #287. Refs #280. Update of accessor method names for core class IPG.

1. Class/file core/IPG.java in api/core/ updated in names of getter

and setter methods for variable 'length', with suffix indicating the unit the value is expressed in. The updated name of the getter method is getLengthInCentiMeters().

2. Classes/files gui/form/FormFactory.java and

action/events/SaveSeparationEvent.java in client/servlet/ updated to comply with the name change. English dictionary has already been updated.

[olle]

(In [2148]) Refs #291. Refs #287. Key strings for text fields and table columns updated to have unit suffix following the same conventions as for getter and setter methods, which makes the dictionary file more consistent.

1. Class/file gui/form/FormFactory.java in client/servlet/ updated

by exchange of "QuantityMicroLiter?" for "QuantityInMicroLiters?".

2. Class/file gui/table/TableFactory.java in client/servlet/ updated

by exchange of "OriginalQuantityMicroLiter?" for "OriginalQuantityInMicroLiters?", and "RemainingQuantityMicroLiter?" for "RemainingQuantityInMicroLiters?".

3. English dictionary file locale/en/dictionary in client/servlet/

updated to use the new string keys.

[olle]

(In [2149]) Refs #287. English localization dictionary file locale/en/dictionary in client/servlet/ updated with entry "EventType?=Event Type".

[olle]

(In [2152]) Refs #287. English localization dictionary file locale/en/dictionary in client/servlet/ updated in order of entries.

[olle]

(In [2157]) Refs #291. Refs #287. Refs #280. Hit class updated in names of some getter and setter methods updated with suffix indicating the unit the value is expressed in. Below the getter methods are listed:

Hit: getDeltaMassInDaltons() and getExperimentalMassInDaltons().

[olle]

(In [2166]) Refs #287. Class/file gui/web/GUIConverter.java in client/servlet/ updated in private method Tag convert(Toolbar toolbar, String formId) to use localized labels for disabled toolbar buttons (previously this was only done for enabled buttons).

[olle]

(In [2167]) Refs #287. Refs #291. Labels updated for localization in form for new separation event:

1. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new valid parameter VFloat VUSEDQUANTITYINMICROLITERS with default label "UsedQuantityInMicroLiters?". Public method <D> Form getForm(Class<D> cls, D obj) updated for class SeparationEvent? to call createField(VUSEDQUANTITYINMICROLITERS) for entry field for used quantity.

2. English localization dictionary file locale/en/dictionary in

client/servlet/ updated with entries for form for new separation event.

[Fredrik Levander]

(In [2175]) Refs #287. Added terms for some new GUI features

[olle]

(In [2176]) Refs #282. Refs #287. Localization updated.

1. English dictionary file updated with entries for single word terms,

in order to use the keys in this dictionary as template for creating dictionaries in other languages.

2. Classes/files gui/form/FormFactory.java and

action/file/ViewActiveFile.java in client/servlet/ updated by exchanging some longer label and legend strings for camel-cased key string to use as keys in the localization dictionary files. English dictionary file updated with the corresponding entries.

[olle]

(In [2177]) Refs #282. Refs #287. Localization updated.

1. English dictionary file updated with entries for single word terms,

in order to use the keys in this dictionary as template for creating dictionaries in other languages.

2. Classes/files gui/form/FormFactory.java and

action/file/ViewActiveFile.java in client/servlet/ updated by exchanging some longer label and legend strings for camel-cased key string to use as keys in the localization dictionary files. English dictionary file updated with the corresponding entries.

[olle]

Note on changesets ​[2176] and ​[2177]:

Changeset ​[2176] refers to the updated dictionary file.

Changeset ​[2177] refers to the updated java source files.

Due to practical concerns, the subversion commit was split into two. The same commit message was used, as the updates are correlated.

[Fredrik Levander]

(In [2178]) Refs #287. Some more new GUI things added to dictionary. Also changed Id to ID in the dictionary

[olle]

(In [2179]) Refs #282. Refs #287. Localization updated.

Classes/files action/hit/ImportHitsWizard.java and action/hit/ListHits.java in client/servlet/ updated by exchanging some longer label and legend strings for camel-cased key string to use as keys in the localization dictionary files. English dictionary file updated with the corresponding entries.

[olle]

(In [2180]) Refs #282. Refs #287. Localization updated.

Classes/files action/directory/ViewActiveDirectory.java, action/project/ViewActiveProject.java and gui/table/TableFactory.java in client/servlet/ updated by exchanging some longer label and legend strings for camel-cased key string to use as keys in the localization dictionary files. English dictionary file updated with the corresponding entries.

[olle]

(In [2188]) Refs #282. Refs #287. Localization updated.

Classes/files action/peakListSet/ListPeakListSet.java, action/sample/ViewActiveSample.java and action/spectrumSearch/ListSpectrumSearches.java in client/servlet updated by exchanging some longer label and legend strings for camel-cased key string to use as keys in the localization dictionary files. English dictionary file updated with the corresponding entries, plus a number of basic key entries.

[olle]

(In [2194]) Refs #282. Refs #287. Class/file gui/form/FormFactory.java in client/servlet/ updated in private method Select<VString> selectPlateId(DbControl? dc, Project project) by exchanging label "ExternalPlateId?" for "PlateExternalId?". Since the label refers to an external id for a plate, the latter label is less prone to misunderstanding, while "ExternalPlateId?" can be interpreted either as "ExternalPlate? Id" or "External PlateId?". The English dictionary file has already been updated with the string key "PlateExternalId?".

[olle]

(In [2231]) "Refs #287. Refs #280. Update of labels to include unit.

1. Class/file action/extract/NewPooledExtract.java in

client/servlet/ updated in labels to include the desired unit.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

(In [2232]) Refs #282. Refs #287. Refs #290. Removed localization from class/file action/hit/ClearHits.java in client/servlet/. This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file action/hit/ClearHits.java in in client/servlet/ updated

by removing localization. Confirmation question string exchanged for string key for question.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

(In [2234]) Refs #282. Refs #287. Refs #290. Removed localization from class/file action/hit/ImportHitsStep1.java in client/servlet/. This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file action/hit/ImportHitsStep1.java in in client/servlet/

updated by removing localization.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

(In [2241]) Refs #282. Refs #287. Removed localization from class/file action/plugin/ListPluginDefinitions.java in client/servlet/.

1. Class/file action/plugin/ListPluginDefinitions.java in

client/servlet/ updated by removing localization. Label string "In extensions" exchanged for string key.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

(In [2242]) Refs #282. Refs #287. Refs #290. Removed some localization from class/file action/project/CreateLargeProject.java in client/servlet/. This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file action/project/CreateLargeProject.java in

client/servlet/ updated by removing localization for form legends and button labels. Localization kept where it is combined with other output data in a composed string, e.g. error messages, as these cases cannot be simply handled by GUIConverter, and these strings are not used as keys for icons.

2. English dictionary file locale/en/dictionary in

client/servlet/ updated with new string keys.

[olle]

(In [2243]) Refs #282. Refs #287. Refs #290. Removed some localization from class/file action/project/ListSamplesInProject.java in client/servlet/. This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file action/project/ListSamplesInProject.java in

client/servlet/ updated by removing localization for button labels. Localization kept where it is combined with other output data in a composed string, e.g. table titles, as these cases cannot be simply handled by GUIConverter, and these strings are not used as keys for icons.

[olle]

(In [2244]) Refs #282. Refs #287. Removed localization from class/file action/read/PermissionDeniedView.java in client/servlet/.

1. Class/file action/read/PermissionDeniedView.java in

client/servlet/ updated by removing localization.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key.

[olle]

(In [2246]) Refs #282. Refs #287. Removed some localization from class/file action/read/ViewAbout.java in client/servlet/.

1. Class/file action/read/Viewabout.java in client/servlet/ updated

by removing localization for window title. Label string "Server Information" exchanged for string key.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [2254]) Refs #282. Refs #287. Refs #290. Removed localization from class/file action/write/ConfirmAction.java in client/servlet/. This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file action/write/ConfirmAction.java in in client/servlet/

updated by removing localization.

2. English dictionary file locale/en/dictionary in client/servlet

updated with new string keys.

[olle]

(In [2256]) Refs #282. Refs #287. Class/file action/hit/ClearHits.java in client/servlet/ updated by setting confirmation question string to "Do you want to clear hits (data will be lost)?" instead of question string key "ClearHitsQuestion?", thus reverting this change made in changeset ​[2232]. The change was reverted as the receiving action action/write/ConfirmAction.java in client/servlet/ uses the string in the contents part of a titled window, and this is currently not processed for localization.

[olle]

(In [2259]) Refs #282. Refs #287. Refs #290. Removed localization from class/file gui/form/FormFactory.java in client/servlet/. This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file gui/form/FormFactory.java in in client/servlet/

updated by removing localization. Some longer label/legend strings exchanged for string label keys.

2. English dictionary file locale/en/dictionary in client/servlet

updated with new string keys.

[olle]

(In [2263]) Refs #287. Refs #290. Class/file action/gel/ListGels.java in client/servlet/ updated by exchanging some button label for label string key. This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file action/gel/ListGel.java in client/servlet/ updated by exchanging some button label for label string key.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

(In [2265]) Refs #287. Refs #290. Class/file action/project/ListMyProjects.java in client/servlet/ updated by exchanging some button label for label string key. This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file action/project/ListMyProjects.java in client/servlet/

updated by exchanging some button label for label string key.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key.

[olle]

(In [2276]) Refs #287. Refs #290. Class/file gui/form/FormFactory.java in client/servlet/ updated in public method Form getMyProfilePropertiesForm(User user) by exchanging button label "Save properties" for label string key "SaveProperties?". This makes it possible to add icons to buttons by referring to the label string key of the button.

1. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getMyProfilePropertiesForm(User user) by exchanging button label "Save properties" for label string key "SaveProperties?".

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entry for string key "SaveProperties?".

3. Default icon settings file "default" in icons/ in client/servlet/

updated with icon assignment for "SaveProperties?" button.

[olle]

(In [2291]) Refs #287. Refs #290. Classes/files action/news/ListNews.java and action/user/ListUsers.java in client/servlet/ updated by exchanging some button labels for label string keys. This makes it possible to add icons to buttons by referring to the label string keys of the buttons.

1. Classes/files action/news/ListNews.java and

action/user/ListUsers.java in client/servlet/ updated by exchanging some button labels for label string keys.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with the new string keys.

3. Default icon settings file "default" in icons/ in client/servlet/

updated with icon assignments for the new string keys.

[olle]

(In [2293]) Refs #287. Refs #290. Class/file action/user/ListUsers.java in client/servlet/ updated by exchanging some button labels for label string keys. This makes it possible to add icons to buttons by referring to the label string keys of the buttons.

1. Class/file action/user/ListUsers.java in client/servlet/ updated

by exchanging some button labels for label string keys.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with the new string keys.

[olle]

(In [2295]) Refs #287. Localization updated.

1. Class/file gui/form/FormFactory.java in client/servlet/ updated

by exchanging longer label and legend strings for camel-cased key strings to use as keys in the localization dictionary files. In some cases where a label or legend string is a combination of fixed strings and variable values, localization of the fixed strings are performed in FormFactory?.

2. English dictionary file updated with the corresponding entries, plus a number of basic key entries. Some previous entries have had

their values changed to better correspond to the key strings. In cases where sometimes a short string is desired, new string key entries have been added for the shorter string values.

3. Class/file gui/table/TableFactory.java in client/servlet/ updated

in private method void initializeColumnNameToUse() to use alternative column name string keys when a shorter column name is desired. This is most often used in case of tables with many columns, e.g. the Hits Report table for the Hit.class, where names like "Spot", "Spectrum", "Plate", and "Well" are preferred over "Spot ID", "Spectrum ID", "Plate ID", and "Well position".

[olle]

(In [2297]) Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with entries for labels and column names for tables accessed by the root user, specifically "News" and "Roles" administration. The names of different Role items have not been added in the dictionary.

[Gregory Vincic]

(In [2335]) Refs #287. Changing titles to use the unlocalized subtitle.

[Gregory Vincic]

(In [2338]) Refs #287. Tables can now also contain an unlocalized subtitle.

[Fredrik Levander]

(In [2340]) Refs #287. Changed some titles and labels

[Fredrik Levander]

(In [2344]) Refs #287. Refs #167. Some changes to layout of active spectrum search, and some localisation

[Fredrik Levander]

(In [2345]) Refs #287. Run Plugin is now Run import plugin

[olle]

Ticket closed as the basic set of labels and headers have correct English localization.

[olle]

(In [2367]) Refs #242. Refs #287. First revision of showing number of pending jobs on the Jobs list page.

1. Class/file action/job/ListJobs.java in client/servlet/ updated in

public method void runMe() by showing the number of jobs that have not ended, in a table below the main job table.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key "PendingJobs?".

[olle]

(In [2368]) Refs #262. Refs #287. First revision of functionality for viewing and restoring items in the trashcan.

1. Class/file action/read/ViewHome.java in client/servlet/ updated

in public method void runMe() by adding action link to new action class ListTrash?.class coupled to toolbar button with label string key "ViewTrash?".

2. New action class/file action/read/ListTrash.java in

client/servlet/, that shows tables with File and Job items tagged for removal. Each table has an added action link to new action class RestoreItems?.class coupled to toolbar button with label string key "Restore".

3. New action class/file action/write/RestoreItems.java in

client/servlet/, that restores selected items in the corresponding trashcan table. This class is based on DeleteItems?.java, but with the functionality reversed.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [2373]) Refs #329. Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key "Labeled".

[olle]

(In [2375]) Refs #245. Refs #287. Refs #290. Adding localization entry and icon for toolbar button "DeleteDirectory?".

1. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

2. Default icon settings file "default" in icons/ in client/servlet/

updated with icon assignments for string key "DeleteDirectory?".

[olle]

Changeset added 2007-11-21 11:27:26 by olle:

(In ​[2408]) Refs #251. Toolbar creation moved from methods getMyProfilePropertiesForm(User user) and getMyProfilePasswordForm(User user) in FormFactory to action classes.

1. Class/file gui/form/FormFactory.java in client/servlet/

updated in public methods Form getMyProfilePropertiesForm(User user) and Form getMyProfilePasswordForm(User user) by removing toolbar creation.

2. Class/file action/user/ViewMyProfileAction.java in client/servlet/

updated in public method void runMe() by creating toolbars for properties form, and password form.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key "ChangePassword".

[olle]

(In [2421]) Refs #265. Refs #287. IPG list page updated in title by exchange of "IPGs" for the more explanatory "IPGs (Immobilized pH Gradients)". Only the page title is changed, table header and menu link title still uses the short version.

1. Class/file action/ipg/ListIPGs.java in client/servlet/ updated in

protected method void runMe() by exchanging page title key string "IPGs" for "IPGsLongVersion".

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key "IPGsLongVersion".

[olle]

(In [2431]) Refs #315. Refs #287. First version of general Protocol editor/viewer.

1. Class/file gui/form/FormFactory.java in client/servlet/ updated:
2. New valid parameters defined.
3. New public method Form getFileProtocolTypeForm(ProtocolType? protocolType).
4. Public method Form getForm(Class cls, Object obj) updated for Protocol.class.

2. Class/file gui/table/TableFactory.java in client/servlet/ updated

in public method void useColumnsFromClass() for Protcol.class to use new readers ProtocolFileNameReader? and ProtocolTypeNameReader?.

3. New reader classes/files props/ProtocolFileNameReader.java and

props/ProtocolTypeNameReader.java in client/servlet/.

4. Class/file action/file/SelectProtocolType.java in client/servlet/

updated in protected method void runMe() to use form obtained by calling new FormFactory? method getFileProtocolTypeForm(null) instead of getForm(ProtocolType?.class, null). This avoids unused name and description fields to be shown, when creating a protocol from a File item.

5. Class/file action/file/CreateProtocolFromFile.java in

client/servlet/ updated in protected method void runMe() to set the file for the created protocol.

6. New class/file action/project/ListProtocolsInProject.java in

client/servlet/, that complements new class/file action/protocol/ListProtocols.java.

7. New action classes/files for managing protocols, placed in new

directory action/protocols/ in client/servlet:

1. AddProtocol?.java
2. ListProtocols?.java
3. NewProtocol?.java
4. ResetProtocolFile?.java
5. SaveProtocol?.java
6. SelectProtocolFileStep1a.java
7. SelectProtocolFileStep1b.java
8. ViewActiveProtocol?.java
9. ViewProtocol?.java
10. ViewProtocolFile?.java

8. Class/file action/read/ViewLeft.java in client/servlet updated

in private method Node createSystemTree(DbControl? dc, User user) by adding node for listing protocol for active project or all protocols.

9. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

[olle]

(In [2440]) Refs #316. Refs #287. Link to protocol view added to event view actions.

1. Class/file action/event/ViewActiveGelScanEvent.java in

client/servlet/ updated in protected method void runMe() by adding toolbar button "View Protocol" coupled to ActionLink? to ViewActiveProtocol?.class for viewing event protocol.

2. Class/file action/event/ViewActiveSeparationEvent.java in

client/servlet/ updated in protected method void runMe() by adding toolbar button "View Protocol" coupled to ActionLink? to ViewActiveProtocol?.class for viewing event protocol.

3. Class/file action/event/ViewActiveStainingEvent.java in

client/servlet/ updated in protected method void runMe() by adding toolbar button "View Protocol" coupled to ActionLink? to ViewActiveProtocol?.class for viewing event protocol.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key "ViewProtocol?".

[olle]

(In [2455]) Refs #315. Refs #287. Creation of protocol from file updated to allow protocol name and description to be selected together with protocol type. As this interfere with the previous option for creating protocols for several files in one step, providing only that the protocol types were equal, creation of protocol from file is now restricted to work only when a single file is selected.

1. Class/file action/file/SelectProtocolType.java in client/servlet/

updated in protected method void runMe() to return an error message if not a single file is selected, and use form obtained by calling new FormFactory? method getFileProtocolForm(file, null) instead of getFileProtocolTypeForm(null). This allows name and description values to be selected. This strictly makes the class name "SelectProtocolType?" inappropriate ("SelectFileProtocol?" would be a better choice), but is not changed here.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

by addition of new public method Form getFileProtocolForm(File file, ProtocolType? protocolType), that returns a form for selecting protocol properties and the name and description field values initially are set to the corresponding values for the file.

3. Class/file action/file/CreateProtocolFromFile.java in

client/servlet/ updated in protected method void runMe() to return an error message if not a single file is selected, and to obtain the protocol name and description from valid parameters.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

[olle]

(In [2461]) Refs #315. Refs #287. English dictionary file updated for changes in changeset ​[2458].

1. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key "ViewProtocolFile?".

[olle]

(In [2464]) Refs #315. Refs #316. Refs #317. Refs #287. Protocol viewing updated to handle protocols tagged for removal.

1. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getForm(Class cls, Object obj) for Protocol.class, by adding a text field for the 'removed' tag if the input object differs from null.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

in private convenience method Select<VInteger> getProtocolSelectBox(Class cls, Object obj). If a protocol is attached to the input object, this protocol now always appear in the select box and is shown as the selected item, even if the protocol is tagged to be removed. However, no other protocols tagged to be removed are shown.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys for "yes" and "no" for future use.

[olle]

(In [2491]) Refs #303. Refs #287. First revision of support for further dividing extracts and labeled extracts.

1. Class/file action/extract/ViewActiveExtract.java in

client/servlet/ updated in protected method void runMe() by adding button coupled to action link to new action NewSecondaryExtract?.class.

2. Class/file action/extract/ViewActiveLabeledExtract.java in

client/servlet/ updated in protected method void runMe() by adding button coupled to action link to new action NewSecondaryLabeledExtract?.class.

3. New classes/files action/extract/NewSecondaryExtract.java and

action/extract/AddSecondaryExtract.java in client/servlet/ for displaying a form to create a secondary extract from a source extract.

4. New classes/files action/extract/NewSecondaryLabeledExtract.java

and action/extract/AddSecondaryLabeledExtract.java in client/servlet/ for displaying a form to create a secondary labeled extract from a source labeled extract.

5. Class/file gui/form/FormFactory.java in client/servlet/ updated by

addition of new public methods related to creation of secondary extracts: Fieldset getUsedLabeledExtractFieldset(LabeledExtract? extract), Form getSecondaryExtractForm(Extract extract, Extract fromExtract), and Form getSecondaryLabeledExtractForm(LabeledExtract? extract, DbControl? dc, LabeledExtract? fromExtract). They are based on previous forms for creating an extract from a sample and a labeled extract from an extract.

6. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [2528]) Refs #376. Refs #287. Support has been added for using an alternative name of the "Next" button in the file selection form. The button name was changed to "Import" for the three file selection steps performed when using the Hits Import Wizard.

1. Class/file gui/form/FormFactory.java in client/servlet updated:
2. New valid parameter VString VFILESELECTIONNEXTBUTTONNAME added.
3. New private method

TextField?<String> newHiddenFileSelectionNextButtonNameField() for storing a button name coupled to valid parameter VString VFILESELECTIONNEXTBUTTONNAME in the form.

3. Hits Import Wizard form public methods

Form getImportHitsWizardStep1Form(Project project), Form getImportHitsWizardStep2Form(Project project), and Form getImportHitsWizardStep3Form(Project project) updated by setting "Next" button name to "Import" for the file selection forms.

2. Class/file action/directory/ViewActiveDirectory.java in

client/servlet/ updated in protected method void runMe() in case of file selection forms, by retrieving an alternative name for the "Next" button from valid parameter VString VFILESELECTIONNEXTBUTTONNAME, and using this if it is not null or an empty string.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key "Import".

[olle]

(In [2554]) Refs #371. Refs #374. Refs #287. Servlet part of support for storage location field for biomaterials added.

1. Class/file gui/form/FormFactory.java in client/servlet/ updated:
2. New valid parameter VString VSTORAGELOCATION for transfer of

storage location values.

2. New private method TextField?<String> newStorageLocationField()

for creation a text input field coupled to valid parameter VString VSTORAGELOCATION.

3. Support for a storage location text field for inspection/input

of storage location data has been added to the following methods:

• public Form getSampleForm(Sample sample)
• public Form getExtractForm(Extract extract)
• public Form getSecondaryExtractForm(Extract extract, Extract fromExtract)
• public Form getLabeledExtractForm(LabeledExtract? extract, DbControl? dc, Extract fromExtract)
• public Form getSecondaryLabeledExtractForm(LabeledExtract? extract, DbControl? dc, LabeledExtract? fromExtract)

2. Action classes/files in client/servlet/ for saving properties

for a MeasuredBioMaterial? have been updated to save storage location data:

• action/sample/AddSample.java
• action/sample/SaveSample.java
• action/extract/AddExtract.java
• action/extract/SaveExtract.java
• action/extract/AddSecondaryExtract.java
• action/extract/AddLabeledExtract.java
• action/extract/SaveLabeledExtract.java
• action/extract/AddSecondaryLabeledExtract.java

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key "StorageLocation?".

[olle]

(In [2576]) Refs #241. Refs #287. Refs #290. First test of support for selection check boxes in directory table in directory inspection form:

1. New class/file DirectoryContext?.java in client/servlet,

constructed in analogy with FileContext?.java.

2. Class/file action/directory/ViewActiveDirectory.java in

client/servlet/ updated to support extensions both for Directory and File items, selected in tables:

1. Protected method void runMe() updated by adding an extensions

button to directory table tool bar, for extensions using the new DirectoryContext?. File table extensions button renamed, to clarify the difference.

2. Private method

Table createDirectoryTable(Table templateTable, Directory dir, Boolean select, Boolean selectMoveDir) updated by not removing initial check box column.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for string keys "ExtensionsForDirectories?" and "ExtensionsForFiles?".

4. Default icon settings file "default" in icons/ in client/servlet/

updated with icon assignments for the new string keys.

5. New extension action/directory/TestExtensionForDirectories.java

in client/servlet/ added for testing selection of directories using check boxes in a directory table. If no directory is selected, an error message is displayed. If one or more directories are selected, it writes a debug comment in the log file for each directory.

[olle]

(In [2594]) Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for string keys "Directories" and "Owner".

[olle]

(In [2615]) Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In [2631]) Refs #391. Refs #287. First revision of functionality for deleting SpectrumSearches? from the GUI:

1. Class/file action/spectrumSearch/ListSpectrumSearches.java in

client/servlet/ updated in public method void runMe() to not configure TableFactory? to hide the id check box column for the SpectrumSearch? table.

2. Class/file gui/table/TableFactory.java in client/servlet/

updated in public method <D extends BasicItem?> Toolbar getBasicTableToolbar(Table tbl) to add a "Delete" button coupled to action link to action DeleteItems?.class to SpectrumSearch? tables.

3. Class/file action/read/ViewHome.java in client/servlet/ updated

in public method void runMe() to count the number of SpectrumSearch? items marked for deletion and call updated FormFactory? method getTrashCanForm(dirCount, fileCount, jobCount, spectrumSearchCount) to get the trash can form.

4. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getTrashCanForm(Integer dirCount, Integer fileCount, Integer jobCount, Integer spectrumSearchCount) with extra argument Integer spectrumSearchCount. The number of SpectrumSearch? items marked for deletion is reported, if > 0.

5. Class/file action/read/ListTrash.java in client/servlet/ updated

in public method void runMe() to show a separate table of SpectrumSearch? items marked for deletion.

6. Class/file action/write/EmptyTrash.java in client/servlet/

updated in protected method void runMe() by including spectrum searches when trying to remove items marked to be deleted.

7. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In [2643]) Refs #404. Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys related to spectrum file types.

[olle]

(In [2647]) Refs #404. Refs #287. Refs #406. Spectrum file reader factory updated with support for PKL peak list files.

1. Class/file action/file/SpectrumFileReaderFactory.java in

client/servlet/ updated with support for PKL peak list files.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2648]) Refs #404. Refs #287. Refs #407. Spectrum file reader factory updated with support for MGF peak list files.

1. Class/file action/file/SpectrumFileReaderFactory.java in

client/servlet/ updated with support for MGF peak list files.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2654]) Refs #404. Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In [2661]) Refs #362. Refs #363. Refs #287. First revision of X!Tandem search in Proteios via web interface to GPM web site.

1. Class/file gui/table/TableFactory.java in client/servlet/

updated in public method void useColumnsFromClass() by obtaining parameter file for XTandemParameterSetStorage item.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new methods related to forms for X!Tandem search:

1. Private method Select<VString> newStringSelectBox(VString validParam, List<String> optionList, String selected).
2. Private method Select<VString> newStringSelectBox2(VString validParam, List<Option> optionList, String selected).
3. Public method Form getNewXTandemParameterSetStorageForm(XTandemParameterSetStorage xTandemParameterSetStorage).
4. Public method Form getXTandemParameterSetForm(XTandemParameterSet xTandemParameterSet).

3. Class/file action/read/ViewLeft.java in client/servlet/ updated

by adding node for viewing XTandemParameterSetStorage items.

4. New core extension class/file

action/file/UseSpectrumFileForXTandemSearchExtension.java in client/servlet/ added, for creating X!Tandem search jobs for selected spectrum files.

5. New action classes/files added to action/xTandemInput/ in

client/servlet/ for creating, viewing, and editing X!Tandem parameter sets and starting X!Tandem search jobs from them:

1. AddXTandemParameterSetStorage.java.
2. ListXTandemParameterSetStorage.java.
3. NewXTandemParameterSetStorage.java.
4. SaveXTandemParameterSetStorage.java.
5. SearchXTandem.java.
6. SelectXTandemParameterFileStep1a.java.
7. SelectXTandemParameterFileStep1b.java.
8. ViewActiveXTandemParameterFile.java.
9. ViewActiveXTandemParameterSetStorage.java.
10. ViewXTandemParameterFile.java.
11. ViewXTandemParameterSetStorage.java.

6. New plugin class/file plugins/SearchXTandemPlugin.java in plugin/

for executing an X!Tandem search via web interface and trying to upload the output XML file into Proteios.

7. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2672]) Refs #410. Refs #287. Refs #290. Separation of view and download options for files:

1. Class/file action/file/ViewActiveFile.java in client/servlet/

updated in public method void runMe():

1. "View/Download?" button replaced by buttons "View" and "Download",

both with an action link to ShowFile?.class, but differing in the value of added parameter ShowFile?.VDOWNLOAD (values "false" and "true", respectively).

2. Decision logic for whether a file is viewable inside Proteios

copied from class/file action/file/ShowFile.java in client/servlet/.

3. If the file contents cannot be viewed inside Proteios, the "View"

button is disabled (dimmed).

2. Class/file action/file/ShowFile.java in client/servlet/ updated

in public method void runMe() by using the value of valid parameter VBoolean VDOWNLOAD to control whether to prepare the file contents to be shown or downloaded (values "false" and "true", respectively). In case the value of parameter VDOWNLOAD or the file item's MIME type is null, download is prepared, as this is the safest option.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

4. Default icon settings file "default" in icons/ in client/servlet/

updated with icon assignment for various string keys.

[olle]

(In [2677]) Refs #362. Refs #363. Refs #287. X!Tandem search updated for use of locally installed search engine (currently for test purposes only).

1. Class/file se/lu/thep/waf/Event.java in api/waf/ updated by

addition of new public method String fetchTempDirPath() for obtaining the path to directory for temporary files from configuration parameter value.

2. Class/file/

action/xTandemInput/ViewActiveXTandemParameterSetStorage.java in client/servlet/ updated in public method void runMe() by setting value of valid parameter SearchXTandem.VSAVEXTANDEMPARAMETERSETFLAG to "true" for commented-out action link to perform X!Tandem search using locally installed search engine, and some other minor changes.

3. Class/file action/xTandemInput/SearchXTandem.java in

client/servlet/ updated in protected method void runMe():

1. Path to directory for temporary files obtained by calling

getEvent().fetchTempDirPath().

2. Use of search engine via web interface is set as default.
3. Bug fixed when creating output path when more than one spectrum

file are used (previously only the first search result was stored in a result file correctly named using the output path base name).

4. Spectrum path is now created using the directory for temporary

files.

4. Class/file plugins/SearchXTandemPlugin.java in plugin/ updated in

private method void xTandemSearchLocal(...) by saving a copy of the spectrum file item in the directory for temporary files. Description of imported result file updated to correspond to description of imported result file when performing X!Tandem search via web interface. Obsolete private method void saveTemporaryFile(java.io.File inFile, java.io.File tmpFile) removed, as it is replaced by polymorphic private method void saveTemporaryFile(File inFile, java.io.File tmpFile).

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2714]) Refs #404. Refs #287. Spectrum file reader factory updated to give a valid file type title when the file argument is null:

1. Class/file action/file/SpectrumFileReaderFactory.java in

client/servlet/ updated in public method String fetchFileTypeTitleString(File file) to return an informative title when the file argument is null.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with entry for string key "MissingFile?".

[olle]

(In [2724]) Refs #392. Refs #287. Refs #290. First revision of support for import of non-gel search results to hits report:

1. Class/file action/hit/ListHits.java in client/servlet/ updated

in public method void runMe() by addition of new toolbar button coupled to action link to new class/file action/hit/ImportHitsNonGelWizard.java in client/servlet/.

2. New class/file action/hit/ImportHitsNonGelWizard.java in

client/servlet/ that calls FormFactory? methods getImportHitsNonGelWizardStep1Form(project) and getImportHitsNonGelWizardStep2Form(project) to obtain the forms for the two import steps. The latter are coupled to action links to new classes/files action/hit/ImportHitsNonGelWizardStep1a.java and action/hit/ImportHitsNonGelWizardStep2a.java in client/servlet/, respectively.

3. New class/file action/hit/ImportHitsNonGelWizardStep1a.java in

client/servlet/ that checks input local sample id before redirecting action to select peaklist files.

4. New class/file action/hit/ImportHitsNonGelWizardStep1b.java in

client/servlet/ that starts a job using new class/file plugins/PeakListToHitNonGelPlugin.java in plugin/ for registering peaklist files for specified local sample id.

5. New class/file action/hit/ImportHitsNonGelWizardStep2a.java in

client/servlet/ that checks input data before redirecting action to select search result files.

6. New class/file action/hit/ImportHitsNonGelWizardStep2b.java in

client/servlet/ that starts a job using class/file plugins/SearchResultsImporter.java in plugin/ for importing search results.

7. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new public methods Form getImportHitsNonGelWizardStep1Form(Project project) and public Form getImportHitsNonGelWizardStep2Form(Project project), together with private convenience methods Select<VString> selectLocalSampleId(DbControl? dc, Project project) and TextField?<String> getLocalSampleIdField(boolean isRequired).

8. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

9. Default icon settings file "default" in icons/ in client/servlet/

updated with icon assignment for non-gel hits import wizard button.

10. New class/file plugins/PeakListToHitNonGelPlugin.java in plugin

for registering peaklist files for specified local sample id.

11. Class/file plugins/SearchResultsImporter.java in plugin/

updated in private method void execute(Request request, Response response, ProgressReporter? progress) by copying values for local sample id and fraction id together with other properties for hit.

[olle]

(In [2730]) Refs #435. Refs #287. First revision of support for obtaining standard alternatives for search parameter values from the used GPM site:

1. Class/file action/xTandemInput

ViewActiveXTandemParameterSetStorage.java in client/servlet/ updated:

1. Public method void runMe() updated to obtain standard

alternatives for search parameter values from the used GPM site, and give these as arguments when calling FormFactory? method getXTandemParameterSetForm(...) to retrieve a form. All tool bar buttons related to saving X!Tandem parameter data are now coupled to an action link to class SaveXTandemParameterSetStorage.class, while values for valid parameters SearchXTandem.VSAVEXTANDEMPARAMETERSETFLAG, FormFactory?.VFWDACTION, and SearchXTandem.VXTANDEMUSEWEBINTERFACEFLAG are added as parameters to the action link to control the branching when forwarding the action.

2. New private convenience method

List<Option> stringListToOptionList(List<String> stringList) added. It converts a list of alternating key and value strings into a list of options.

2. Class/file gui/form/FormFactory.java in client/servlet/

updated:

1. Public method

Form getXTandemParameterSetForm(XTandemParameterSet xTandemParameterSet) by adding new arguments for option lists with parameter value alternatives, Form getXTandemParameterSetForm(XTandemParameterSet xTandemParameterSet, List<Option> listPathDefaultParametersOptionList, List<Option> speciesOptionList, List<Option> proSpeciesOptionList, List<Option> residueModificationMassOptionList, List<Option> residuePotentialModificationMassOptionList, List<Option> proteinCleavageSiteOptionList, List<Option> refinePotentialModificationMassOptionList), that are used in select boxes. Select boxes for multiple selection and the possibility to specify ones own value instead of selecting an item in a select box has been added (values selected in a select box will only be used if no own value has been entered). Selection of protein taxon is divided into two select boxes for multiple selection, one for Eukaryotes and one for Prokaryotes.

2. New private convenience method

boolean itemInOptionList(List<Option> optionList, String item) added. It checks if a string is found as option value in an option list.

3. New private convenience method

boolean allItemsInOptionList(List<Option> optionList, List<String> itemList) added. It checks if all strings in input list are found as option values in an option list.

4. New private convenience method

Select<VString> newStringMultipleSelectBox(VString validParam, List<Option> optionList, List<String> selectedList) added. It returns a select box for selecting a list of string values.

5. New private convenience method

List<String> listStringToStringList(String listString, String delimiterRegex) added. It converts a list String to a list with String elements.

3. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java

in client/servlet/ updated:

1. Protected method void runMe() updated to only save an X!Tandem

parameter set retrieved from the HTTP request if value of valid parameter VBoolean SearchXTandem.VSAVEXTANDEMPARAMETERSETFLAG is true. Values for valid parameters VInteger SearchXTandem.VSPECTRUMFILEID and VBoolean SearchXTandem.VXTANDEMUSEWEBINTERFACEFLAG are retrieved, so the values can be used for added parameters for forward action.

2. Public method XTandemParameterSet fetchCurrentXTandemParameterSe

() updated to support select boxes for multiple selections, and the possibility to specify ones own value instead of selecting an item in a select box. Selections from multiple selection select boxes for Eukaryote and Prokaryote taxons are combined into one multiple taxon selection. String lists from multiple selection select boxes are processed by new private method List<String> uniqueStringItemList(...) to remove redundancies, and are then converted by new private method String stringListToListString(...) into a string with the list items delimited by commas, for use in XML tag value fields.

3. New private convenience method

List<String> uniqueStringItemList(List<String> stringList) added. It converts a list with String elements to a list with unique String elements by removing duplicate elements.

4. New private convenience method

String stringListToListString(List<String> stringList, String delimiterString) added. It converts a list with String elements to a list String with chosen delimiter string between elements.

4. Class/file action/xTandemInput/SearchXTandem.java in

client/servlet/ updated:

1. Protected method void runMe() updated to retrieve the

X!Tandem parameter set from the used X!Tandem parameter set storage item, instead of from the HTTP request by calling private method XTandemParameterSet fetchCurrentXTandemParameterSet().

2. Private method

XTandemParameterSet fetchCurrentXTandemParameterSet() has been removed, since it is no longer used. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java in client/servlet/ now retrieves the values from the HTTP request, and stores them in the used X!Tandem parameter set storage item.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2743]) Refs #404. Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with string key entries originally added in changeset ​[2654], that were later unintentionally removed during sorting, as they contained a '#' character in the entries and therefore was filtered out. Filter command for sorting updated to only remove lines starting with a '#' character, i.e. comment lines.

[olle]

(In [2747]) Refs #364. Refs #287. First revision of selection of grouping annotation for DIGE Analyzer:

1. New class/file action/file/DecyderXMLtoDIGEAnalyzerExtension.java

in client/servlet/, that shows a select box with annotation names for Samples, Extracts, and LabeledExtracts?. As the importer class/file the extension was designed for, plugins/DecyderXMLtoDIGEAnalyzer.java in plugin/, uses "group" as default value for the annotation name, this is always added as first item in the select box. Selected file id values are transferred together with the annotation name string to new action class/file action/file/DecyderXMLtoDIGEAnalyzerJobCreator.java in client/servlet/.

2. New class/file action/file/DecyderXMLtoDIGEAnalyzerJobCreator.java

in client/servlet/, that retrieves the selected file id values and annotation name and creates one import job per file, with the annotation name set as job parameter. The jobs are configured to be executed by class/file plugins/DecyderXMLtoDIGEAnalyzer.java in plugin/.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2751]) Refs #442. Refs #356. Refs #287. The "File" menu is extended with a new "Select project" hierarchical menu at the top, where one can select/de-select an active project. The currently selected menu item is marked with a bullet icon:

1. Class/file gui/Node.java in client/servlet/ updated by addition

of new private String instance variable iconPath with public accessor methods. The default value of iconPath is null.

2. Class/file gui/web/GUIConverter.java in client/servlet/ updated

in public method Tag convert(Node node) by adding an icon image on the left side of a menu item if the value of String instance variable iconPath for the menu node is different from null. In this case the image corresponding to the iconPath value is used. As a special case, if the icon path corresponds to the "blankbutton.gif" 1x16 pixels spacer image, the image attributes will be set to 10x14 pixels, to be used as spacer for bullet image "checkedmenu.gif", which has the latter dimensions.

3. Class/file gui/MainMenu.java in client/servlet/ updated:
4. Private method Node createFileNode() by adding a project

selection hierarchical menu node at the top. The project selection menu node is created by new private convenience method createSelectProjectNode().

2. New private convenience method Node createSelectProjectNode()

for creating the hierarchical project selection menu. The first menu item is reserved for the case when no active project is selected, and is coupled to an action link to action DeactivateProject?.class for de-selecting an active project. Menu items for projects are coupled to action links to new action SelectActiveProject?.class for making the selected project active. An initial icon image to the left of a menu item for marking what item is selected is obtained by calling new private convenience method String fetchSelectionIconPath(boolean selected).

3. New private convenience method

String fetchSelectionIconPath(boolean selected) for obtaining the path to an icon image indicating if the current menu item is selected or not. A bullet icon is used to indicate that a menu item is selected.

4. New class/file action/project/SelectActiveProject.java in

client/servlet/ that retrieves the value of valid parameter VInteger FormFactory?.VID and makes the project with this id value to the active project, and then forwards the action to ViewHome?.class.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2783]) Refs #448. Refs #257. Refs #287. First version of support for managing user preferences from the GUI, containing user preferences for e-mail notification of job completion:

1. Class/file gui/MainMenu.java in client/servlet/ updated in

private method Node createFileNode() by adding node for user preferences in File menu, coupled to action link to new action class ViewPreferences?.class.

2. New class/file action/preferences/ViewPreferences.java in

client/servlet/ that obtains notification configuration data and calls new public FormFactory? method Form getNotificationConfigurationForm(NotificationConfiguration? nc) to get a form displaying the values. The form is equipped with a button coupled to an action link to new action SavePreferences?.class for saving changed values for user preference variables.

3. Class/file gui/form/FormFactory.java in client/servlet/ updated

by addition of new public method Form getNotificationConfigurationForm(NotificationConfiguration? nc) for displaying notification configuration values. It calls new private method Select<VInteger> getNotificationModeSelectBox(int modeValue) to obtain a select box for the notification mode.

4. New class/file action/preferences/SavePreferences.java in

client/servlet/ that obtains preferences from HTTP request via valid parameters and stores the values in the user's preference file, after which the action is forwarded to new action ViewPreferences?.class.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2830]) Refs #453. Refs #287. Initial filter for listing plugins set to new filter class MinimalAttributeFilter, which displays columns for id, name, plugin version, and contact information:

1. New filter class/file core/MinimalAttributeFilter.java in

api/core/ that implements the AttributeFilter interface. It displays columns for id, name, plugin version, and contact information.

2. Class/file action/plugin/ListPluginDefinitions.java in

client/servlet/ updated in public method void runMe() by setting the value of valid parameter VString VFILTERCLASS to the name of new filter class MinimalAttributeFilter, before forwarding the action to class ConfigureTableFactory2.

3. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In ​[2835]) Refs #458. Refs #362. Refs #363. Support added for inspecting and editing new X!Tandem search parameters related to scoring algorithm:

1. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java

in client/servlet/ updated:

1. New valid parameters added corresponding to X!Tandem settings

"spectrum, use conditioning" and "scoring, algorithm".

2. Public method XTandemParameterSet fetchCurrentXTandemParameterSet()

updated by retrieving the values corresponding to X!Tandem settings "spectrum, use conditioning" and "scoring, algorithm" from valid parameters.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getXTandemParameterSetForm(...) by adding select box for inspecting and setting the value corresponding to "scoring, algorithm". Default value is an empty string, which is displayed as option "native" in the select box.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2898]) Refs #456. Refs #287. First revision of Mascot result retrieval in Proteios via web interface to Mascot web site.

1. New core extension class/file

action/directory/MascotResultRetrievalExtension.java in client/servlet/ added, for creating Mascot result retrieval jobs for uploading desired result files to selected directory. It calls FormFactory? public method Form getMascotResultRetrievalForm(Directory dir) to display a form for entering Mascot result retrieval parameters, after which the action is forwarded to class/file action/file/MascotResultRetrieval.java in client/servlet/.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new public method Form getMascotResultRetrievalForm(Directory dir) related to form for Mascot result retrieval.

3. New class/file action/file/MascotResultRetrieval.java in

client/servlet/ added. It retrieves parameter values from valid parameters and creates one Mascot result retrieval job for each Mascot search number, using new plugin MascotResultRetrievalPlugin.

4. New plugin class/file plugins/MascotResultRetrievalPlugin.java

in plugin/ for retrieving a result file for a Mascot search via web interface and upload the output XML file into Proteios.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2906]) Refs #481. Refs #362. Refs #363. Refs #287. First revision of support for "Save As..." functionality when editing an X!Tandem Parameter Set:

1. Class/file action/xTandemInput/SearchXTandem.java in

client/servlet/ updated with new valid parameter VBoolean VSAVEASXTANDEMPARAMETERSETFLAG.

2. Class/file

action/xTandemInput/ViewActiveXTandemParameterSetStorage.java in client/servlet/ updated in public method void runMe() to add "Save As..." button coupled to action link to SaveXTandemParameterSetStorage.class, and setting value of added parameter VBoolean VSAVEASXTANDEMPARAMETERSETFLAG to true.

3. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java

in client/servlet/ updated in protected method void runMe() with support for "Save As..." functionality. It calls new public FormFactory? method Form getSaveAsXTandemParameterSetStorageForm( XTandemParameterSetStorage xTandemParameterSetStorage, XTandemParameterSet xTandemParameterSet) to obtain a form for setting properties for a new X!Tandem parameter set tot store the data in.

4. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new public method Form getSaveAsXTandemParameterSetStorageForm( XTandemParameterSetStorage xTandemParameterSetStorage, XTandemParameterSet xTandemParameterSet) for getting a form for setting properties for a new X!Tandem parameter set tot store the data in. Also new convenience methods public Fieldset addXTandemParameterSetToFieldset( XTandemParameterSet xTandemParameterSet, Fieldset fs, boolean fieldsHidden, boolean fieldsDisabled) etc. for storing values of X!Tandem parameters in hidden fields coupled to valid parameters.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2917]) Refs #471. Refs #356. Refs #287. First revision of OMSSA search in Proteios via locally installed search engine.

1. Class/file gui/table/TableFactory.java in client/servlet/

updated in public method void useColumnsFromClass() by obtaining parameter file for OMSSAParameterSetStorage item.

2. Class/file gui/form/FormFactory.java in client/servlet/

updated with new methods related to forms for OMSSA search:

1. Public method Form getNewOMSSAParameterSetStorageForm

(OMSSAParameterSetStorage omssaParameterSetStorage).

2. Public method Form getSaveAsOMSSAParameterSetStorageForm

(OMSSAParameterSetStorage omssaParameterSetStorage, OMSSAParameterSet omssaParameterSet).

3. Public method Fieldset addOMSSAParameterSetToFieldset

(OMSSAParameterSet omssaParameterSet, Fieldset fs, boolean fieldsHidden, boolean fieldsDisabled).

4. Public method Fieldset addVStringParameterToFieldset

(VString vStringParameter, String value, Fieldset fs, boolean fieldsHidden, boolean fieldsDisabled).

5. public Form getOMSSAParameterSetForm

(OMSSAParameterSet omssaParameterSet, List<Option> enzymeOptionList, List<Option> sequenceLibraryOptionList, List<Option> speciesOptionList, List<Option> fixedModsOptionList, List<Option> variableModsOptionList).

3. Class/file gui/MainMenu.java in client/servlet/ updated by

adding node for viewing search setup items under the View menu. The current X!Tandem menu item is moved here, and the new OMSSA menu item is also placed here.

4. New core extension class/file

action/file/UseSpectrumFileForOMSSASearchExtension.java in client/servlet/ added, for creating OMSSA search jobs for selected spectrum files.

5. New action classes/files added to action/omssa/ in

client/servlet/ for creating, viewing, and editing OMSSA parameter sets and starting OMSSA search jobs from them:

1. AddOMSSAParameterSetStorage.java.
2. ListOMSSAParameterSetStorage.java.
3. NewOMSSAParameterSetStorage.java.
4. SaveOMSSAParameterSetStorage.java.
5. SearchOMSSA.java.
6. SelectOMSSAParameterFileStep1a.java.
7. SelectOMSSAParameterFileStep1b.java.
8. ViewActiveOMSSAParameterFile.java.
9. ViewActiveOMSSAParameterSetStorage.java.
10. ViewOMSSAParameterFile.java.
11. ViewOMSSAParameterSetStorage.java.

6. New plugin class/file plugins/SearchOMSSAPlugin.java in

plugin/ for executing an OMSSA search via a locally installed search engine and trying to upload the output XML file into Proteios.

7. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2928]) Refs #482. Refs #287. Function "Export to File" for exporting table data to a file updated to ask the user whether only the shown data or all data should be exported:

1. Class/file action/file/ExportToFile.java in client/servlet/

updated:

1. The class now implements the ContextEnabled interface.
2. New public valid parameter VBoolean VEXPORTALLITEMS added.
3. Protected method void runMe() updated to check if value of

valid parameter VBoolean VEXPORTALLITEMS is true, in which case the query is modified to export all data.

4. New private static instance variable List<Context> contexts

with public getter method List<Context> listContexts().

5. New public static method TitledWindow createExportModeForm()

for creating the content of the new export mode popup dialog.

2. Class/file action/ConfigureTableFactory2.java in client/servlet/

updated to couple button "Export to File" to a popup link with content created by calling new public static method TitledWindow createExportModeForm() in class/file action/file/ExportToFile.java in client/servlet/. If the value of valid parameter VBoolean VEXPORTALLITEMS is null, which is the default value, no extra action is initiated, while if it is true or false, indicating that action has been returned from the export mode popup dialog, the action is forwarded to action ExportToFile, together with valid parameter VBoolean VEXPORTALLITEMS.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2941]) Refs #483. Refs #287. First revision of PIKE search in Proteios via web interface.

1. New core extension class/file

action/file/UseProteinListFileForPIKESearchExtension.java in client/servlet/ added, for creating PIKE search jobs for selected protein list files.

2. Class/file gui/form/FormFactory.java in client/servlet/

updated with new method related to form for PIKE search:

1. Public method Form getPIKEParameterSetForm(

String pikeUserName, String pikeUserMail, String pikeSourceDatabase, List<String> pikeFieldSelectList, String pikeGeneOntologyCheck, String pikeMaxDeep, String pikeInputFileType, List<String> pikeOutputFileTypeList, List<Option> sourceDatabaseOptionList, List<Option> fieldSelectOptionList, List<Option> inputFileTypeOptionList, List<Option> outputFileTypeOptionList).

3. New action class/file SearchPIKE.java added to action/pike/

in client/servlet/ for starting PIKE search job performed by new class/file plugins/SearchPIKEPlugin.java in plugin/.

4. New plugin class/file plugins/SearchPIKEPlugin.java in

plugin/ for executing a PIKE search via web interface and trying to upload the result file(s) into Proteios.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2973]) Refs #405. Refs #287. First experimental revision of exporting Hits table data to PRIDE XML files:

1. New class/file action/hit/PrideExport.java in client/servlet/

that is connected to new button "PrideExportBtn?" in the Hits table tool bar. It constructs a default output filename prefix with timestamp and then calls new FormFactory method getPrideExportForm(Project project, String filenamePrefixDefault) to obtain a form with settings for exporting Hits table data to PRIDE XML files. The "Next" button of the form forwards the action to new class CreatePrideExportJob.

2. Class/file gui/form/FormFactory.java updated with new

public method Form getPrideExportForm(Project project, String filenamePrefixDefault) for obtaining a form with settings for exporting Hits table data to PRIDE XML files.

3. New class/file action/hit/CreatePrideExportJob.java in

client/servlet/ that retrieves export settings from values of valid parameters and then creates one job for each peaklist file in the Hits table. The plugin related to the jobs is set to new plugin class PrideExportPlugin, and retrieved export settings are transferred to the jobs as job parameter values.

4. New class/file plugins/PrideExportPlugin.java in plugin/

that obtains input values from job parameter values, gets Hits item data from a query of the Hits database table, and exports data to a PRIDE XML file.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [2976]) Refs #405. Refs #287. PRIDE XML version number is now reported in the TITLE XML block of the PRIDE XML file, and the PRIDE XML export form header title. The PRIDE XML version that is currently supported by Proteios SE is 2.1.

1. Class/file plugins/PrideExportPlugin.java in plugin/ updated in

private method void writePrideXmlHeader(XMLCrudeWriterImpl xmlCrudeWriterImpl) by reporting the PRIDE XML version number.

2. English dictionary file locale/en/dictionary in client/servlet/

updated by adding the PRIDE XML version number in the PRIDE XML export form header title.

[olle]

(In [2985]) Refs #504. Refs #287. First version of routine for setting same file type for several files:

1. New class/file action/file/SetFileTypeExtension.java in

client/servlet/ that calls new public FormFactory method Form getFileTypeForm(DbControl? dc, File file) for obtaining a form for selecting a file type, after which the action is forwarded to new action class SetFileType.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new public method Form getFileTypeForm(DbControl? dc, File file) for obtaining a form for selecting a file type.

3. New class/file action/file/SetFileType.java in client/servlet/

that obtains the selected files and file type from valid parameters and sets the file types of the files to the one selected, after which the action is forwarded to action class ViewActiveDirectory.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3010]) Refs #405. Refs #287. PRIDE XML export updated for gel based export with option to append the gel external id to the optional output filename prefix:

1. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getPrideExportForm(Project project, String filenamePrefixDefault) by adding a check box in the output field set for selecting to append the gel external id to the optional output filename prefix. The check box is checked by default, and is coupled to new valid parameter VBoolean VGELEXTERNALIDPREFIX in class/file action/hit/CreatePrideExportJob.java in client/servlet/.

2. Class/file action/hit/CreatePrideExportJob.java in

client/servlet/ updated with new valid parameter VBoolean VGELEXTERNALIDPREFIX. Its value is obtained from the form created by FormFactory? public method Form getPrideExportForm(Project project, String filenamePrefixDefault). If the flag and a gel external id has been chosen, the gel external id is appended to the originally selected filename prefix, and transferred to the created job.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new entry for the string key for the check box.

[olle]

(In [3023]) Refs #405. Refs #287. The PRIDE XML version number displayed in the PRIDE XML export form header title is now taken from the same source as the version number written in the TITLE XML block of the PRIDE XML file. A single source is therefore now used for the PRIDE XML version number, and it need not be referenced in the dictionary files. This is an update to the changes made in changeset ​[2976].

1. Class/file plugins/PrideExportPlugin.java in plugin/ updated

by changing string constant PRIDE_XML_VERSION_STR from a private environment variable to a public static variable.

2. Class/file action/hit/PrideExport.java in client/servlet/

updated in protected method void runMe() by getting PRIDE XML version number from static variable PrideExportPlugin.PRIDE_XML_VERSION_STR.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key entry and removal of references to the PRIDE XML version number in string keys.

[olle]

(In [3035]) Refs #405. Refs #287. PRIDE XML export is updated to allow a local sample id to be appended to the export filename prefix in case of non-gel based export:

1. Class/file action/hit/CreatePrideExportJob.java in

client/servlet/ updated for appending an extra id to the filename prefix:

1. Name of valid parameter VBoolean VGELEXTERNALIDPREFIX changed

to VBoolean VEXTRAPREFIX to reflect that the extra prefix may be either a gel external id or a local sample id.

2. Protected method void runMe() updated to use either a gel

external id or a local sample id as optional extra prefix, depending on whether the export is gel based or non-gel based. Relevant variable names changed to not refer specifically to a gel external id.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getPrideExportForm(Project project, String filenamePrefixDefault) by change of variable name for check box indicating extra id prefix, and exchanging check box label key string AppendGelExternalIdToPrefix for the more appropriate AppendExtraIdToPrefix.

3. English dictionary file locale/en/dictionary in client/servlet/

updated by exchanging check box string key AppendGelExternalIdToPrefix for AppendExtraIdToPrefix and changing the text to cover both gel based and non-gel based PRIDE XML export.

[olle]

(In [3046]) Refs #500. Refs #163. Refs #287. First support of allowing selection of score types to combine in combined hits report:

1. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getCombineHitsForm(Project project) by use of three field sets instead of one, where the second one contains new score type select boxes for each available score type, with alternatives "Not used", "E-value", and "Score". The score types and their settings are transferred via VString valid parameters to class/file action/hit/CombineHits.java in client/servlet/.

2. Class/file action/hit/CombineHits.java in client/servlet/

updated in protected method void runMe() by obtaining the lists of score type names and score type settings from values of the VString valid parameters. New String lists are created that only contain the entries for the score types that were selected to be used. The new lists are transferred as StringParameterType parameter values to the job created.

3. Class/file plugins/CombinedHitsReport.java in plugin/ updated

in public method void run(Request request, Response response, ProgressReporter? progress) by obtaining the string lists of score types and their settings from job parameters, and creating String and boolean arrays score_types and compareE, respectively, with values corresponding to the obtained list data.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3082]) Refs #405. Refs #287. Refs #290. PRIDE XML export updated to allow selection of an optional PRIDE XML protocol file from which to copy the protocol XML block from:

1. Class action/hit/PrideExport.java in client/servlet/ updated

by forwarding action to new class SelectPrideProtocolFileStep1a instead of CreatePrideExportJob. Name of "Next" button updated.

2. New class/file action/hit/SelectPrideProtocolFileStep1a.java

in client/servlet/ added. It retrieves values from valid parameters and stores them as session attributes, after which it forwards the action to class ViewActiveDirectory for optional selection of a PRIDE protocol file.

3. New class/file action/hit/SelectPrideProtocolFileStep1b.java

in client/servlet/ added. It retrieves the id for an optional PRIDE protocol file from a valid parameter and stores it as session attribute, after which it forwards the action to class CreatePrideExportJob.

4. Class/file action/hit/CreatePrideExportJob.java in

client/servlet/ updated by retrieving parameter values from session parameters. Also transfer value of optional id for PRIDE protocol file to created job.

5. Class/file plugins/PrideExportPlugin.java in plugin/ updated.
6. Public method

void run(Request request, Response response, ProgressReporter? progress) update3d to retrieve optional PRIDE protocol XML file.

2. Private method

void writePrideXmlHeader(XMLCrudeWriterImpl xmlCrudeWriterImpl) updated to check if a PRIDE protocol XML file is specified, and if its is valid according to the PRIDE protocol XSD, copies its protocol XML block to the created PRIDE XML file.

3. Private convenience method

void copyMzDataXMLBlocks(XMLCrudeWriterImpl xmlCrudeWriterImpl, Integer aPeakListFileId) exchanged for more general convenience method void copySelectedXMLBlocks(XMLCrudeWriterImpl xmlCrudeWriterImpl, Integer sourceFileId, String selectedXmlTagName) for copying a specified XML block from an XML file.

4. New private convenience methods

boolean xmlFileValidation(Integer xmlFileId, String xsdFilePathToUse, String xmlTypeName) and boolean xmlFileValidation(File xmlFile, String xsdFilePathToUse, String xmlTypeName) added, for checking if an XML file item is valid according to a specified XML Schema Definition (XSD) file.

6. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys. Warning message regarding experimental status of PRIDE XML export removed.

7. Default icon settings file "default" in icons/ in client/servlet/

updated with icon assignments for various string keys.

[olle]

(In [3088]) Refs #512. Refs #356. Refs #287. Active project menu updated to have shorter cascade menus for Hits items:

1. Class/file gui/MainMenu.java in client/servlet/ updated to

replace the current "Hits" cascade menu in the active project menu by the sub-menus to the former.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3160]) Refs #518. Refs #517. Refs #287. Refs #290. First revision of support for aborting jobs:

1. Class/file action/job/ListJobs.java in client/servlet/ updated

in public method void runMe() by addition of new "Abort" button coupled to action link to new action AbortJobs.

2. New class/file action/job/AbortJobs.java in client/servlet added.

It retrieves a list of job id values from valid parameters and calls new public method boolean abort() in class Job for waiting and executing job items. It returns a fairly detailed info message regarding what action was performed for different types of jobs.

3. Interface/file core/plugin/Response.java in api/core/ updated:
4. New public method void setAborted() added.
5. New public method void setAborted(String message) added.
6. Public enum Status updated with new entry ABORTED.
7. Java-doc comments updated to current style standard.

4. Class/file core/PluginResponse.java in api/core/ updated:
5. New public method void setAborted() added.
6. New public method void setAborted(String message) added.

5. Class/file core/Job.java in api/core/ updated:
6. New public method AbortableJobQueueInterface getAbortableJobQueue()

added. It calls static method Application.getAbortableJobQueueHashMap()` to retrieve the abortable job queue (if any) for the job.

2. New public method PluginExecutionRequest getPluginExecutionRequest()

added. If the job queue manager implements interface AbortableJobQueueInterface, it calls public method PluginExecutionRequest getPluginExecutionRequest(int jobId) in the job queue manager to retrieve the result.

3. Public enum Status extended with two new entries ABORTING

and ABORTED.

4. New public method void doneAborted(String statusMessage) added.

This method is used to update the job properties for a waiting job that has been aborted (an executing job that terminates due to it being aborted calls new public Response method void setAborted(...)).

5. Method void setEnded(PluginResponse response) updated to

handle new Response status value Response.Status.ABORTED.

6. New public method boolean abort() added. This is the main

method handling an aborted job command. Where appropriate, it updates status value for the job, notifies the plugin that the job command has been aborted, and adds the job id to the aborted job id list.

7. New public method void removeAbortedJobId(int jobId) added.

It removes job id from the aborted job id list.

8. New public method boolean jobCommandAborted() added.

It checks if the job command is aborted.

6. Class/file core/SimpleJobQueue.java in api/core/ updated to

implement interface AbortableJobQueueInterface and manage aborted jobs in the internal job queue:

1. New private instance variable

HashMap<Integer,PluginExecutionRequest> pluginExecutionRequestHashMap added with private accessor method HashMap<Integer,PluginExecutionRequest> getPluginExecutionRequestHashMap() that creates a new hash map if none exists.

2. Public method PluginExecutionRequest getPluginExecutionRequest(int jobId)

added (part of interface AbortableJobQueueInterface).

3. New private instance variable List<Integer> abortedJobIdList

added.

4. Public methods List<Integer> getAbortedJobIdList(),

void addAbortedJobId(int jobId), void removeAbortedJobId(int jobId), and boolean isJobCommandAborted(int jobId) added. All are part of interface AbortableJobQueueInterface.

5. Private method void removeNonWaitingJobsFromQueue() renamed

removeFinishedJobsFromQueue() and modified to remove queue job items that have other status than WAITING, EXECUTING, or ABORTING. Note that it is not the database status value for the job item that is inspected, but the status value of the job object in the internal job queue. This will remove job objects in the queue with status value updated to ABORTED, and will therefore stop them from being executed, even if the job was loaded to the job queue before the job command was executed.

6. New private method void updateStatusForAbortedJobsInQueue()

added. It updates status for jobs in queue if they are listed to be aborted.

7. Public method void run() updated to call new private method

updateStatusForAbortedJobsInQueue() before removeFinishedJobsFromQueue(), in order to make the latter method remove already aborted job items from the internal job queue, and stop them from being executed.

8. Private method void runNextJobInQueue() updated to set the

status of a job in the job queue to EXECUTING after the job is started.

1. Additions to existing methods in order to keep the hash map for job id and PluginExecutionRequest up to date.

7. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

8. Default icon settings file "default" in icons/ in client/servlet/ updated with icon assignments for various string keys.

[olle]

(In [3194]) Refs #536. Refs #287. First version of support for inspection of contact and instrument information in mzData and mzML spectrum files:

1. New interface/file io/SpectrumFileContactInterface.java in

api/core/ added.

2. New class/file io/SpectrumFileContact.java in api/core/

added, that implements SpectrumFileContactInterface.

3. New interface/file io/SpectrumFileContactReaderInterface.java

in api/core/ added.

4. New interface/file io/SpectrumFileInstrumentInterface.java

in api/core/ added.

5. New class/file io/SpectrumFileInstrument.java in api/core/

added, that implements SpectrumFileInstrumentInterface.

6. New interface/file io/SpectrumFileAnalyzerInterface.java in

api/core/ added.

7. New class/file io/SpectrumFileAnalyzer.java in api/core/

added, that implements SpectrumFileAnalyzerInterface.

8. New interface/file io/SpectrumFileInstrumentReaderInterface.java

in api/core/ added.

9. New interface/file io/StringPairInterface.java in api/core/

added, intended to simplify transfer of name/value pair data.

10. New class/file io/StringPair.java in api/core/ added,

that implements StringPairInterface.

11. Class/file io/PeakListFileImpl.java in api/core/ updated

to implement SpectrumFileContactReaderInterface and SpectrumFileInstrumentReaderInterface, when reading data from mzData spectrum files.

12. Class/file io/MzMLFileReader.java in api/core/ updated

to implement SpectrumFileContactReaderInterface and SpectrumFileInstrumentReaderInterface, when reading data from mzML spectrum files.

13. Class/file action/file/SpectrumFileReaderFactory.java in

client/servlet/ updated by adding public methods SpectrumFileContactReaderInterface fetchSpectrumFileContactReader(File file) and SpectrumFileInstrumentReaderInterface fetchSpectrumFileInstrumentReader(File file). The new methods will return readers for mzData and mzML spectrum files, else null.

14. Class/file gui/form/FormFactory.java in client/servlet/

updated by adding new public methods Form getSpectrumFileContactForm(SpectrumFileContact spectrumContact) and Form getSpectrumFileInstrumentForm(List<SpectrumFileInstrumentInterface> spectrumFileInstrumentList), as well as private convenience method `void addTableRow(Table table, String nameKey, Object value, Class<? extends ProteiosAction?> actionClass, int itemId)` to add a new row entry to a table.

15. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3195]) Refs #536. Refs #287. Class/file plugins/SearchResultsImporter.java in plugin/ reverted to previous version, since the changes were erroneously committed in changeset ​[3194] in connection with adding support forinspection of contact and instrument information in mzData and mzML spectrum files.

[olle]

(In [3205]) Refs #515. Refs #287. First version of support for editing of sample and contact information in mzData and mxML spectrum files:

1. New class/file action/file/SpectrumFileContactDataAdderExtension.java

in client/servlet/ added. It calls new FormFactory public method Form getSpectrumFileContactInputForm(Project project, String outputDirNameDefault) to obtain contact info, that is transfered to new class SpectrumFileContactDataAdder.

2. New class/file action/file/SpectrumFileContactDataAdder.java

in client/servlet/ added. It obtains contact data from values of valid parameters and creates one job per supported spectrum file. It also creates the output directory, if not already existing.

3. New class/file action/file/SpectrumFileSampleDataAdderExtension.java

in client/servlet/ added. It calls new FormFactory public method Form getSpectrumFileSampleInputForm(Project project, String outputDirNameDefault) to obtain sample info, that is transfered to new class SpectrumFileSampleDataAdder.

4. New class/file action/file/SpectrumFileSampleDataAdder.java

in client/servlet/ added. It obtains sample data from values of valid parameters and creates one job per supported spectrum file. It also creates the output directory, if not already existing.

5. Class/file gui/form/FormFactory.java in client/servlet/ updated:
6. New public method

Form getSpectrumFileContactInputForm(Project project, String outputDirNameDefault) added for obtaining contact data for spectrum files.

2. New public method

Form getSpectrumFileSampleInputForm(Project project, String outputDirNameDefault) added for obtaining sample data for spectrum files.

6. New class/file plugins/MzDataContactDataAdderPlugin.java in

plugin. It adds contact info to an mzData spectrum file.

7. New class/file plugins/MzMLContactDataAdderPlugin.java in

plugin. It adds contact info to an mzML spectrum file.

8. New class/file plugins/MzDataSampleDataAdderPlugin.java in

plugin. It adds sample info to an mzData spectrum file.

9. New class/file plugins/MzMLSampleDataAdderPlugin.java in

plugin. It adds sample info to an mzML spectrum file.

10. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3213]) Refs #517. Refs #287. Job table page updated to show the number of pending jobs for each job queue, in addition to the total number of pending jobs:

1. Class/file action/job/ListJobs.java in client/servlet/ updated

in public method void runMe() by getting the number of pending jobs for each job queue, and displaying the result after the total number of pending jobs.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3214]) Refs #517. Refs #287. Update intended to clarify job queue descriptions:

1. Class/file core/JobQueueManager.java in api/core/ updated in

protected method synchronized void start() by clarifying job queue descriptions.

2. Class/file action/job/ListJobs.java in client/servlet/ updated

in public method void runMe() by identifying a job queue from what job estimated execution times it is intended for, instead of using the id string for the job queue. Also, strings used to specify the job queues on the Job table page have been modified, as have some variable names related to the job queues.

3. English dictionary file locale/en/dictionary in client/servlet/

updated by exchange of some entries related to job queues.

[olle]

(In [3216]) Refs #517. Refs #287. Support for putting selected jobs into a high priority job queue added:

1. Interface/file core/ManageableJobQueueInterface.java in api/core/

extended with new public method void remove(JobData jobData).

2. Class/file core/BasicJobQueue.java in api/core/ extended with

new public method void remove(JobData jobData).

3. Class/file core/JobQueueManager.java in api/core/ updated:
4. Protected synchronized method void start() updated by

creating a high priority queue, in addition to the fast-job and slow-job queues.

2. New public method void putJobInHighPriorityQueue(Job job)

added, that calls new private method void forceBlockerToQueue(ManageableJobQueueInterface jobQueue, JobData jobData) to put the job into the high priority job queue.

3. New private method

void forceBlockerToQueue(ManageableJobQueueInterface jobQueue, JobData jobData) added. It is based on private method void addBlockerOf(ManageableJobQueueInterface jobQueue, JobData jobData), but if a job is already loaded into another job queue, it is first removed from that queue, before being added to the new job queue.

4. Class/file action/job/ListJobs.java in client/servlet/ updated

in public method void runMe() by displaying the number of pending jobs also for the new high priority job queue, and addition of new tool bar button coupled to action link to new action PutJobsInHighPriorityQueue.class.

5. New class/file action/job/PutJobsInHighPriorityQueue.java in

client/servlet/ added. It obtains a list of id values for selected job items, and then calls new public method void putJobInHighPriorityQueue(Job job) in JobQueueManager to put the selected jobs into the high priority job queue.

6. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3279]) Refs #554. Refs #287. Refs #290. File properties form extended with a new "Original search results" tool-bar button for inspecting original search results, when the file type indicates a Mascot or X!Tandem result file:

1. Class/file action/file/ViewActiveFile.java in client/servlet/

updated in public method void runMe() by adding a new "Original search results" tool-bar button, when the file type indicates a Mascot or X!Tandem result file. The button is coupled to an action link to either action ViewOriginalMascotResultsExtension or ViewOriginalXTandemResultsExtension, depending on the file type. The id value of the file item is added to valid parameter FormFactory.VID, thereby giving the same result as if the file had been selected in the file table, and the extension then selected.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with entry for new string key.

3. Default icon settings file "default" in icons/ in

client/servlet/ updated with icon assignment for new string key.

[olle]

(In [3297]) Refs #534. Refs #356. Refs #287. First revision of Mascot search in Proteios via locally installed search engine.

1. Class/file gui/table/TableFactory.java in client/servlet/

updated in public method void useColumnsFromClass() by obtaining name and seacrh type of parameter file for MascotParameterSetStorage item.

2. Class/file gui/form/FormFactory.java in client/servlet/

updated with new methods related to forms for Mascot search:

1. Public method `Form getNewMascotParameterSetStorageForm(

MascotParameterSetStorage? mascotParameterSetStorage)`.

2. Public method `Form getSaveAsMascotParameterSetStorageForm(

MascotParameterSetStorage? mascotParameterSetStorage, MascotParameterSet? mascotParameterSet)`.

3. Public method `Fieldset addMascotParameterSetToFieldset(

MascotParameterSet? mascotParameterSet, Fieldset fs, boolean fieldsHidden, boolean fieldsDisabled)`.

4. Public method Form getMascotSearchUserDataInputForm(User user).
5. Public method `Form getMascotParameterSetForm(

MascotParameterSet? mascotParameterSet, List<Option> enzymeOptionList, List<Option> missedCleavagesOptionList, List<Option> sequenceLibraryOptionList, List<Option> speciesOptionList, List<Option> fixedModsOptionList, List<Option> variableModsOptionList, List<Option> quantitationOptionList, List<Option> peptideTolUnitOptionList, List<Option> peptideIsotopeErrorOptionList, List<Option> msMsTolUnitOptionList, List<Option> peptideChargeOptionList, List<Option> dataFormatOptionList, List<Option> instrumentOptionList, List<Option> reportTopOptionList)`.

3. Class/file gui/MainMenu.java in client/servlet/ updated by

adding new Mascot menu item to the search setup node under the View menu.

4. New core extension class/file

action/file/UseSpectrumFileForMascotSearchExtension.java in client/servlet/ added, for creating Mascot search jobs for selected spectrum files.

5. New action classes/files added to action/mascot/ in

client/servlet/ for creating, viewing, and editing Mascot parameter sets and starting Mascot search jobs from them:

1. AddMascotParameterSetStorage?.java.
2. ListMascotParameterSetStorage?.java.
3. NewMascotParameterSetStorage?.java.
4. SaveMascotParameterSetStorage?.java.
5. SearchMascot?.java.
6. SelectMascotParameterFileStep1a.java.
7. SelectMascotParameterFileStep1b.java.
8. SelectMascotParameterSetStorage?.java.
9. ViewActiveMascotParameterFile?.java.
10. ViewActiveMascotParameterSetStorage?.java.
11. ViewMascotParameterFile?.java.
12. ViewMascotParameterSetStorage?.java.

6. New plugin class/file plugins/SearchMascotPlugin.java in

plugin/ for executing a Mascot search via web interface and trying to upload the output XML file into Proteios.

7. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3321]) Refs #535. Refs #287. Refs #290. First revision of support for comparison of hits report:

1. New class/file action/hit/HitsComparisonReportStep1.java in

client/servlet/ added. It is coupled to new Hits table tool bar button "Hits Comparison Report" via a TableToolbarContext. It displays a form obtained by calling FormFactory new public method Form getHitsComparisonReportProjectSelectionForm(Project project, List<Project> projectList), and then forwards the results and action to new class HitsComparisonReport.

2. New class/file action/hit/HitsComparisonReport.java in

client/servlet/ added. It retrieves parameter values from valid parameters and displays a form obtained by calling FormFactory new public method Form getHitsComparisonReportForm(Project project, Project project1, Project project2, String filenamePrefixDefault). It then forwards the results and action to new class CreateHitsComparisonReportJob.

3. New class/file action/hit/CreateHitsComparisonReportJob.java

in client/servlet/ added. It retrieves parameter values from valid parameters and creates a job using new plug-in class HitsComparisonReportPlugin. Localization strings for hit table columns etc. are transferred to the created job.

4. New class/file plugins/HitsComparisonReportPlugin.java in

plugin/ added. It compares hit lists obtained by database queries for the two selected projects, and stores the result in tables with tab-separated values in a file located in the project directory of the active project.

5. Class/file gui/form/FormFactory.java in client/servlet/ updated:
6. New public method

Form getHitsComparisonReportProjectSelectionForm(Project project, List<Project> projectList) added for selecting two projects to compare hits for.

2. New public method

Form getHitsComparisonReportForm(Project project, Project project1, Project project2, String filenamePrefixDefault) added for selecting various comparison parameter values.

3. New private convenience method

Select<VString> selectMultiSelectionExternalGelId(DbControl dc, Project project, VString vStringParam) added.

4. New public convenience method

Select<VString> selectMultiSelectionLocalSampleId(DbControl dc, Project project, VString vStringParam) added.

5. New public convenience method

Select<VString> selectMultiSelectionFractionId(DbControl dc, Project project, VString vStringParam) added.

6. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

7. Default icon settings file "default" in icons/ in

client/servlet/ updated with icon assignments for various buttons.

[olle]

(In [3325]) Refs #584. Refs #287. Non-gel import updated to check length of fraction id string parsed from filename, and allow optional parsing using entered regex pattern string:

1. Class/file action/hit/ImportHitsNonGelWizardStep1a.java in

client/servlet updated in protected method void runMe() by obtaining values from valid parameters for new variables related to alternative parsing of fraction id from filename using entered regex pattern string. The values are saved as session attributes before forwarding the action.

2. Class/file action/hit/ImportHitsNonGelWizardStep1b.java in

client/servlet updated in protected method void runMe() by obtaining values from session attributes for new variables related to alternative parsing of fraction id from filename using entered regex pattern string. The values are transferred to the created job for plug-in PeakListToHitNonGelPlugin.

3. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getImportHitsNonGelWizardStep1Form(Project project) with a check-box (default unchecked) for choosing to use an entered regex pattern to parse the fraction id from the input filename, and a text entry field for the regex pattern string.

4. Class/file plugins/PeakListToHitNonGelPlugin.java in plugin/

updated in private method void execute(Request request, Response response, ProgressReporter progress):

1. New FilenameParseUtil method

String fetchRegexResult(String inStr, String regexStr) is used to parse fraction id string from filename using entered regex pattern string, if this option has been selected.

2. The length of the parsed fraction id string is always checked to

not exceed the allowed length, before an attempt is made to update the database. If the length is too long, the job terminates with an error message describing the problem, the parsed fraction id string, its length and the allowed max length.

5. Class/file io/FilenameParseUtil.java in api/core/ updated with

new public method String fetchRegexResult(String inStr, String regexStr) for fetching the first capturing group for the regex pattern when applied to the input string.

6. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3327]) Refs #580. Refs #187. Refs #287. Text of button to clear the Hits table and the related warning message updated, in order to clarify that all contents in the Hits table will be removed, not just entries related to search data:

1. Class/file action/hit/ClearHits.java in client/servlet/ updated

in public static method TitledWindow createPermissionForm(Boolean recursive) by exchanging warning text "All hits data will be erased, do you want to continue?" for "All contents of the hits table will be erased, do you want to continue?".

2. English dictionary file locale/en/dictionary in client/servlet/

updated in entries for string keys for the text on button to clear the Hits table, and for the related warning text (the latter localization is currently not used, but the text was updated to be consistent with the warning text in class ClearHits).

[olle]

(In [3341]) Refs #535. Refs #287. Support for comparison of hits report updated by changing some names of input fields, internal variables, and constants to refer to two hit selections instead of two projects:

1. Class/file action/hit/HitsComparisonReportStep1.java in

client/servlet/ updated in protected method void runMe().

2. Class/file action/hit/HitsComparisonReport.java in

client/servlet/ updated in protected method void runMe() and in names of valid parameters.

3. Class/file action/hit/CreateHitsComparisonReportJob.java

in client/servlet/ updated:

1. Protected method void runMe() updated.
2. private List<String> fetchLocalizerKeyList()` updated.

4. Class/file plugins/HitsComparisonReportPlugin.java in

plugin/ updated:

1. Private inner class HitsComparisonData updated.
2. Public method

void run(Request request, Response response, ProgressReporter progress) updated.

3. Public method

void doExport(DbControl dc, HitsComparisonData hcd, File outCoreFile, ProgressReporter progress) updated.

4. Name of private method

List<Hit> fetchProjectHitList(DbControl dc, Project theProject, ...) changed to List<Hit> fetchHitSelectionHitList(DbControl dc, Project theProject, ...).

5. Class/file gui/form/FormFactory.java in client/servlet/ updated:
6. Public method

Form getHitsComparisonReportProjectSelectionForm(Project project, List<Project> projectList) updated.

2. Public method

Form getHitsComparisonReportForm(Project project, Project project1, Project project2, String filenamePrefixDefault) updated.

6. English dictionary file locale/en/dictionary in client/servlet/

updated.

[olle]

(In [3342]) Refs #535. Refs #287. Support for comparison of hits report updated by indicating that selection of fraction id values is optional:

1. Class/file action/hit/HitsComparisonReport.java in

client/servlet/ updated in protected method void runMe().

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getHitsComparisonReportForm(Project project, Project project1, Project project2, String filenamePrefixDefault) .

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key.

[olle]

(In [3343]) Refs #535. Refs #287. Support for comparison of hits report updated by adding menu entry for hits comparison to the sub-menu to cascade menu <active project> -> Reports:

1. Class/file gui/MainMenu.java in client/servlet/ updated in

private method Node createProjectMenu() by adding node for hits comparison.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key.

[olle]

(In [3349]) Refs #535. Refs #287. Support for hits comparison updated:

1. Class/file action/hit/CreateHitsComparisonReportJob.java in

client/servlet/ updated in private method List<String> fetchLocalizerKeyList() by adding string keys.

2. Class/file plugins/HitsComparisonReportPlugin.java in plugin/

updated in public method void doExport(DbControl dc, HitsComparisonData hcd, File outCoreFile, ProgressReporter progress):

1. A summary of the number of hits in each of the three categories,

"A: Common hits", "B: Unique hits for hit selection 1", and "C: Unique hits for hit selection 2", is printed in the report before the tables with hits in each category.

2. The tables with hits in each category now have an initial column

with the category descriptor "A", "B", or "C".

3. English dictionary file locale/en/dictionary in client/servlet/ updated.

[olle]

(In [3351]) Refs #535. Refs #287. Support for hits comparison updated with protein comparison settings:

1. Class/file action/hit/HitsComparisonReport.java in

client/servlet/ updated with new valid parameters for score type and flag to ignore FDR cutoff values.

2. Class/file action/hit/CreateHitsComparisonReportJob.java in

client/servlet/ updated in protected method void runMe() by obtaining values from valid parameters of score type and flag to ignore FDR cutoff values, and transferring the values to the created job via job parameters.

3. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getHitsComparisonReportForm(Project project, Project project1, Project project2, String filenamePrefixDefault) by adding new section for protein comparison settings, with check box for ignoring FDR cutoff values and select box for score type.

4. Class/file plugins/HitsComparisonReportPlugin.java in plugin/

updated:

1. Private inner class HitsComparisonData updated with new

instance variables with accessor methods for score type and flag to ignore FDR cutoff values.

2. Public method

void run(Request request, Response response, ProgressReporter progress) updated to obtain values from job parameters for score type and flag to ignore FDR cutoff, and transferring these values to the created HitsComparisonData object given as argument when calling public method void doExport(DbControl dc, HitsComparisonData hcd, ....

3. Public method

void doExport(DbControl dc, HitsComparisonData hcd, File outCoreFile, ProgressReporter progress) updated to get values from HitsComparisonData argument for score type and flag to ignore FDR cutoff. If the latter flag is set, FDR cutoff values are reset to null. The score type is used as argument when calling updated private method List<Hit> fetchHitSelectionHitList(...).

4. Private method List<Hit> fetchHitSelectionHitList(...)

updated with new argument String scoreTypeStr. The value of scoreTypeStr is used as argument when calling updated private method ItemQuery<Hit> createBasicHitQuery(...).

5. Private method ItemQuery<Hit> createBasicHitQuery(...)

updated with new argument String scoreTypeStr. If the value of scoreTypeStr differs from null, the query is filtered to only include hits with this score type value.

5. English dictionary file locale/en/dictionary in client/servlet/ updated.

[olle]

(In [3367]) Refs #592. Refs #540. Refs #287. First version of support for zoom functionality when inspecting mass spectra in spectrum files:

1. Class/file action/file/InspectActiveSpectrumFile.java in

client/servlet/ updated:

1. New public static final valid parameter VBoolean VKEEPORIGINALSPECTRUM added.
2. Protected method void runMe() updated to obtain mass range

cutoff values from PlotFileSpectrum valid parameters VMASSCUTOFFLOWSTR and VMASSCUTOFFHIGHSTR, as well as flag indicating if the original spectrum should be kept when zooming from valid parameter VKEEPORIGINALSPECTRUM. New FormFactory public method Form getSpectrumMassRangeSelectionForm(String massCutoffLow, String massCutoffHigh, String spectrumId) is called to obtain a spectrum mass range selection form for setting the mass cutoff parameters. When action class PlotFileSpectrum is used to plot the spectrum image, the mass cutoff values are transferred as added parameters. If zoom is used and the flag indicating that the original spectrum should be kept is set, the original spectra is shown above the zoomed one.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new public method Form getSpectrumMassRangeSelectionForm(String massCutoffLow, String massCutoffHigh, String spectrumId). It returns a spectrum mass range selection form for setting the mass cutoff parameters. The value of argument String spectrumId is stored in a valid parameter of a hidden field in the form, in order to be available when the class using the form is called again.

3. Class/file action/peakList/PlotFileSpectrum.java in

client/servlet/ updated:

1. New public static final valid parameters

VString VMASSCUTOFFLOWSTR and VString VMASSCUTOFFHIGHSTR added.

2. Protected method void runMe() updated to obtain values of

mass cutoff values from valid parameters VString VMASSCUTOFFLOWSTR and VString VMASSCUTOFFHIGHSTR, and using these when calling new private method SpectrumInterface zoomSpectrum(SpectrumInterface spectrum, Float massCutoffLow, Float massCutoffHigh) to select mass values before plotting spectrum.

3. New private method

SpectrumInterface zoomSpectrum(SpectrumInterface spectrum, Float massCutoffLow, Float massCutoffHigh) added. It selects mass values allowed by the mass cutoff restrictions and returns a new spectrum containing only these mass peaks.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3381]) Refs #596. Refs #356. Refs #287. First version of administrator view of logged-in users:

1. Class/file core/Application.java in api/core/ updated:
2. New private static map Map<Integer, Date> userLoginTimeMap

added, for storing user id and login time for logged-in users.

2. Static synchronized method void start(boolean installation)

updated with initializing new private static map Map<Integer, Date> userLoginTimeMap.

3. New protected static method void addUserLoginTime(int userId)

added. It adds a user id to user login time map, if the user id is not already in map.

4. New protected static method void removeUserLoginTime(int userId)

added. It removes a user id from user login time map, if the user id is in the map.

5. New public static method List<Integer> fetchLoggedInUserIdList()

added. It fetches a copy of the list of logged-in user id values.

6. New public static method Date fetchUserLoginTime(int userId)

added. It fetches user login time, or null if user not logged in.

7. New public static method

Long fetchUserTimeSinceLastAccessInMilliSeconds(int userId) added. It fetches the time since last access for the user in milliseconds. Returns null if the user is not logged in.

2. Class/file core/Sessioncontrol.java in api/core/ updated:
3. Public synchronized method

void login(String login, String password, String comment, boolean encryptedPassword) updated by calling new protected static method void addUserLoginTime(int userId) in class Application to set login time for user.

2. Public synchronized method void logout() updated by calling

new protected static method void removeUserLoginTime(int userId) in class Application to remove login time entry for user.

3. New public method boolean isLoggedInAdminInfo() added.

It checks if a user is logged in or not. Intended for administrative info only, therefore does not update last access time.

4. New public method int getLoggedInUserIdAdminInfo() added.

It gets the id of the logged in user, or 0 if no user is logged in. Intended for administrative info only, therefore does not update last access time.

3. Class/file gui/MainMenu.java in client/servlet/ updated:
4. Private method Node createViewNode() updated with new menu

node for listing logged-in users. It is only enabled for administrators.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3388]) Refs #603. Refs #287. First version of routine for setting same MIME type for several files:

1. New class/file action/file/SetMimeTypeExtension.java in

client/servlet/ that calls new public FormFactory method Form getMimeTypeForm(DbControl dc, File file) for obtaining a form for selecting a MIME type, after which the action is forwarded to new action class SetMimeType.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated:
3. New public method Form getMimeTypeForm(DbControl? dc, File file)

added. It returns a form for selecting a MIME type. New private method Select<VString> selectMimeType(DbControl dc, File file) is called to obtain a select box for available MIME types.

2. New private method

Select<VString> selectMimeType(DbControl dc, File file) added. It returns a select box for available MIME types, with the default choice set to the MIME type of the input file. If no MIME type is set for the file, an attempt is made to choose the default MIME type from the file extension. If the latter attempt fails, a blank entry will be chosen as default. New public static methods List<MimeTypeData> getMimeTypeDataList(DbControl dc) and String getMimeTypeStringByExtension(DbControl dc, String extension) in class MimeType is called to obtain data for the select box.

3. Class/file core/MimeType.java in api/core/ updated:
4. New public static method

List<MimeTypeData> getMimeTypeDataList(DbControl dc) added. It performs new pre-defined query GET_MIME_TYPE_DATA_LIST to obtain a list of available MIME types.

2. New public static method

String getMimeTypeStringByExtension(DbControl dc, String extension) added. It performs pre-defined query GET_MIME_TYPE_FROM_EXTENSION for the input file extension and returns the obtained MIME type string.

4. XML file conf/common-queries.xml in api/core/ updated with

new pre-defined query GET_MIME_TYPE_DATA_LIST for obtaining a list of available MIME types.

5. New class/file action/file/SetMimeType.java in client/servlet/

added. It obtains the selected files and MIME type from valid parameters and sets the MIME types of the files to the one selected, after which the action is forwarded to action class ViewActiveDirectory.

6. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3421]) Refs #593. Refs #287. First version of batch BioMaterial import.

1. New class/file action/file/BatchImportExtension.java in

client/servlet/ added. It takes a list of selected input files and parses the input using public methods in new plug-in class BatchImportPlugin. The results of the parsing is presented in tables for each input file. If no errors are found, a tool-bar button is shown linked to new action class CreateBatchImportJobs.

2. New class/file action/file/CreateBatchImportJobs.java in

client/servlet/ added. It creates one for each input file using new plug-in class BatchImportPlugin.

3. New class/file plugins/BatchImportPlugin.java in plugin/ added.

It parses the input file, and if no errors are found, tries to import the BioMaterial data.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3426]) Refs #616. Refs #611. Refs #540. Refs #287. Inspection of mass spectra stored in spectrum files updated with buttons to select previous or next spectrum in list:

1. Class/file action/file/InspectActiveSpectrumFile.java in

client/servlet/ updated:

1. Protected method void runMe() updated with new form to

support the tool-bar with two new spectrum iteration buttons in. It will be placed directly below the spectrum plot, above the zoom mass range selection form. The "Previous spectrum" and "Next spectrum" buttons will be coupled to an action link to the spectrum file inspector class, but with value of valid parameter PlotFileSpectrum.VSPECTRUMID set to the spectrum id string for the previous and next spectrum, respectively. The latter spectrum id strings are obtained by calling new convenience methods String fetchPreviousListItem(String currentItem, List<String inList) and String fetchNextListItem(String currentItem, List<String> inList). The button action is disabled if the spectrum id string to use is null, indicating that the start or end of the list is reached.

2. New public convenience method

String fetchPreviousListItem(String currentItem, List<String> inList) added. It fetches the previous list item from the input string list. Returns null if current item is the first item in the list.

3. New public convenience method

String fetchNextListItem(String currentItem, List<String> inList) added. It fetches the next list item from the input string list. Returns null if current item is the last item in the list.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3473]) Refs #612. Refs #209. Refs #287. Basic support for storing files in compressed format internally added:

1. XML file with common queries conf/common-queries.xml in

api/core/ updated with new SQL query "SET_COMPRESSED_ON_FILES" for setting the "compressed" property to false and the "compressedSize" property to current size for all files with a null value.

2. Class/file core/Install.java in api/core/ updated by

changing the value of integer constant NEW_SCHEMA_VERSION from 8 to 9.

3. New class/file core/UpdateToSchemaVersion9.java in api/core/

added. Protected method int adjustItemsToNewSchemaVersion(org.hibernate.Session session) executes pre-defined SQL query SET_COMPRESSED_ON_FILES.

4. New interface/file core/AbsoluteProgressReporter.java in

api/core/ added.

5. New class/file core/SimpleProgressReporter.java in api/core/

added. It implements interrface ProgressReporter.

6. New class/file core/SimpleAbsoluteProgressReporter.java in

api/core added. It extends class SimpleProgressReporter and implements interface AbsoluteProgressReporter.

7. Class/file core/data/FileData.java in api/core/ updated:
8. New private instance variables boolean compressed and

long compressedSize added, together with public accessor methods.

8. Class/file core/File.java in api/core/ updated:
9. New private instance variable boolean uploadCompressed

added. It indicates cases where automatic compression of uploaded files should be used. Default value is false. Currently not used, but added to increase similarity with BASE2 coded and possible future use.

2. New public method void compress(ProgressReporter progress)

added. It compresses the file stored on disk, if not already compressed.

3. New public method void decompress(ProgressReporter progress)

added. It decompresses the file stored on disk if the former is stored in compressed format.

4. New private method

void compressOrDecompress(ProgressReporter progress, boolean compress) added. It compresses or decompresses the file depending on the value of boolean argument compress.

5. New public method boolean isCompressed() added.

It reports if the file is stored in compressed format internally.

6. New public method long getCompressedSizeBytes() added.

It reports the compressed size in bytes of the file. If the file is not stored in compressed format internally, the normal size in bytes of the file is reported.

6. Public method void upload(InputStream in, boolean checkMd5)

updated to call new public method void upload(InputStream in, boolean checkMd5, Boolean compress) with argument compress set to null.

7. New public method

void upload(InputStream in, boolean checkMd5, Boolean compress) added. It calls new public method OutputStream getUploadStream(boolean checkMd5, Boolean compress, boolean append) with argument append set to false.

8. Public method OutputStream getUploadStream(boolean checkMd5)

updated to call new public method OutputStream getUploadStream(boolean checkMd5, Boolean compress, boolean append) with argument compress set to null and argument append set to false.

1. New public method

OutputStream getUploadStream(boolean checkMd5, Boolean compress) added. It calls new public method OutputStream getUploadStream(boolean checkMd5, Boolean compress, boolean append) with argument append set to false.

10. New public method

OutputStream getUploadStream(boolean checkMd5, Boolean compress, boolean append) added. It supports optional storage in compressed format internally.

11. Public method InputStream getDownloadStream(long offset)

updated to decompress the content of a file stored in compressed format internally.

12. New public method

InputStream getRawDownloadStream(long offset) added. It does not attempt to decompress the content of a file stored in compressed format internally.

13. Private method java.io.File getNewFile() updated with

argument boolean compress. If the latter has value true, the name of the internal file is given file extension ".gz".

14. Private inner class UploadStream updated with new

private instance variables java.io.File file and boolean compress. Constructor UploadStream(java.io.File file, boolean calculateMd5, boolean checkMd5, boolean append) updated with new argument boolean compress to UploadStream(java.io.File file, boolean calculateMd5, boolean checkMd5, boolean compress, boolean append). Supports optional storage in compressed format internally.

9. Class/file util/FileUtil.java in api/core/ updated:
10. Public static method long copy(InputStream in, OutputStream out)

updated to call new public static method long copy(InputStream in, OutputStream out, AbsoluteProgressReporter progress) with argument progress set to value null.

2. New public static method

long copy(InputStream in, OutputStream out, AbsoluteProgressReporter progress) added. It supports an optional AbsoluteProgressReporter.

10. Class/file util/ConsoleProgressReporter.java in api/core/

updated:

1. Public method void display(int percent, String message)

updated to display en empty message string if the input message is null.

11. Class/file Service.java in client/servlet/ updated:
12. Private method void createItems(RequestData data)

updated to call method getUploadStream(...) in class File with argument compress set to value null.

12. Class/file plugins/MsInspectSearchResultsToCSVFile.java

in plugin/ updated:

1. Private method

OutputStream getOutputStream(File f, DbControl dc, List<String> oldcontent) updated to call method getUploadStream(...) in class File with argument compress set to value null.

13. Class/file plugins/SearchResultsPepCSVMatch.java in plugin/

updated:

1. Private method

OutputStream getOutputStream(File f, DbControl dc) updated to call method getUploadStream(...) in class File with argument compress set to value null.

14. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3482]) Refs #612. Refs #287. Class/file core/File.java in api/core/ updated by changing name of public getter method long getCompressedSizeBytes() to long getCompressedSizeInBytes(), in order to comply with previous coding principles in Proteios:

1. Class/file core/File.java in api/core/

updated by changing name of public getter method long getCompressedSizeBytes() to long getCompressedSizeInBytes().

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3490]) Refs #377. Refs #287. First version of support for user-defined order of column sorting in tables managed by class ConfigureTableFactory2:

1. Class/file gui/table/Column.java in client/servlet/ updated

with new private intance variable Integer sortPriority with public accessor methods. Default value is null.

2. Class/file gui/web/GUIConverter.java in client/servlet/ updated:
3. Public method Tag convert(org.proteios.gui.table.Table table)

updated. Table configuration pop-up window extended with new column with name key string "ColumnSortPriority", at the right of the "Order By" column. For entries with an order set ("asc" or "desc"), the new column will contain a select box with sort priority options from 1 to the number of entries for which an order can be set, plus a blank option.

3. Class/file action/ConfigureTableFactory2.java in client/servlet/

updated:

1. Public method

List<Column> getHeader(ProteiosAction context, List<AttributeDefinition> attributes) updated to call new private method Map<String, Integer> fetchSortPriorityMap(ProteiosAction context, List<AttributeDefinition> show) to obtain a of column keys versus sort priorities. The map is used to set sort priority values for columns.

2. New private method

`Map<String, Integer> fetchSortPriorityMap(ProteiosAction? context,

List<AttributeDefinition?> show)`

added. It returns a map of column key versus sort priority. Only records used for sorting will be added to the map. Columns with sort priority set will be listed first. Columns with no sort priority set will be listed after that. If necessary, sort priority will be renumbered to start with 1 and increase in steps of 1.

3. Public method

TableFactory2 configure(DbControl dc, Class<?> wrapperClass, ...) updated to call new private method List<Column> fetchColumnsInSortPriorityOrder(List<Column> inputColumns) to obtain a list of columns sorted after sort priority, and use this list when calling public method void orderBy(List<Column> header, ItemQuery query) to apply sorting conditions to the database query used to obtain data for the table.

4. New private method

List<Column> fetchColumnsInSortPriorityOrder(List<Column> inputColumns) added. It returns a list of columns sorted after sort priority.

5. New private convenience method

String arrayAsString(Integer[] integerArr) added for printing an array of integers.

6. New private convenience method

String arrayAsString(String[] stringArr) added for printing an array of strings.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3494]) Refs #164. Refs #287. First version of support for user-defined column display order in tables managed by class ConfigureTableFactory2:

1. Class/file gui/table/Column.java in client/servlet/ updated

with new private instance variable Integer displayOrder with public accessor methods. Default value is null.

2. Class/file gui/web/GUIConverter.java in client/servlet/ updated:
3. Public method Tag convert(org.proteios.gui.table.Table table)

updated. Table configuration pop-up window extended with new column with name key string "ColumnDisplayOrder", at the right of the "Show" column. For entries other than the "Id" index column, the new configuration column will contain a select box with display order options from 1 (if no "Id" column exists) or 2 (if an "Id" column exists) to the number of entries.

3. Class/file action/ConfigureTableFactory2.java in client/servlet/

updated:

1. Private method

Map<String, Integer> fetchSortPriorityMap(ProteiosAction context, List<AttributeDefinition> show) updated with new argument String priorityVariableName, and renamed fetchPriorityMap(...). Argument priorityVariableName will initially support the values "displayOrder" and "sortPriority".

2. Private method

List<Column> fetchColumnsInSortPriorityOrder(List<Column> inputColumns) updated with new argument String priorityVariableName, and renamed fetchColumnsInPriorityOrder(...). Argument priorityVariableName will initially support the values "displayOrder" and "sortPriority".

3. Public method

List<Column> getHeader(ProteiosAction context, List<AttributeDefinition> attributes) updated to call private method Map<String, Integer> fetchPriorityMap(ProteiosAction context, List<AttributeDefinition> show, String priorityVariableName) to obtain maps of column keys versus display order values and sort priorities. The maps are used to set display order and sort priority values for columns.

4. Public method

TableFactory2 configure(DbControl dc, Class<?> wrapperClass, ...) updated to call private method List<Column> fetchColumnsInPriorityOrder(List<Column> inputColumns, String priorityVariableName) to obtain lists of columns sorted after display order and sort priority. The list sorted after column display order replaces the default column list.

4. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3497]) Refs #582. Refs #287. Basic support for storing table preferences added, but without functionality to tables:

1. Class/file core/PreferencesFile.java in api/core updated;
2. New private instance variable int tablePreferencesMode and

List<TablePreferences> tablePreferencesList with public accessor methods added.

2. Private method void fetchPreferences() updated with call

to new private method void fetchTablePreferences().

3. New private method void fetchTablePreferences() added.

It fetches user preferences for tables from user preferences file and stores them in instance variables.

4. New private convenience method

List<String> listStringToStringList(String listStr, String separator) added. It creates a string list from a list string.

5. New public method void resetTablePreferences() added.

It resets the table preferences list.

6. Public method void save() updated with call to new

private method void saveTablePreferences().

7. New private method void saveTablePreferences() added.

It saves table preferences in user preferences file.

8. New private convenience method String valueString(Object input)

added. It returns the input value as string if not null, else an empty string.

2. New class/file io/ColumnPreferences.java in api/core/ added.

It stores temporary values of preferences for a column.

3. New class/file io/TablePreferences.java in api/core/ added.

It stores temporary values of preferences for a table.

4. New class/file io/TablePreferencesConfiguration.java in

api/core/ added. It stores temporary values of configuration settings for table preferences.

5. Class/file io/NotificationConfiguration.java in api/core/

updated by removing debug output that would be undesirably long when the preferences file is used to store table preferences.

6. Class/file action/preferences/ViewPreferences.java in

client/servlet/ updated:

1. Public method void runMe() updated to obtain table

preferences configuration from the preferences file and call new FormFactory method Form getUserPreferencesConfigurationForm( NotificationConfiguration nc, TablePreferencesConfiguration tpc) to obtain a form to display.

7. Class/file gui/form/FormFactory.java in client/servlet/

updated:

1. New public method

Form getUserPreferencesConfigurationForm( NotificationConfiguration nc, TablePreferencesConfiguration tpc) added. It calls new private methods for obtaining Fieldsets for notifaction and table preferences configuration, and returns a form for user preferences configuration settings.

2. Public method

Form getNotificationConfigurationForm(NotificationConfiguration nc) changed to return a Fieldset instead of a Form, Fieldset getNotificationConfigurationFieldset(NotificationConfiguration nc)

3. New public method

Fieldset getTablePreferencesConfigurationFieldset(TablePreferencesConfiguration tpc) added. It returns a Fieldset for table preferences configuration settings.

4. New private method

Select<VInteger> getTablePreferencesModeSelectBox(int modeValue) added. It creates a select box for table preferences mode.

8. Class/file action/preferences/SavePreferences.java in

client/servlet/ updated:

1. New valid parameters VBoolean VTABLEPREFERENCESRESET and

VInteger VTABLEPREFERENCESMODE added, for obtaining values of table preferences reset flag and usage mode, respectively.

2. Public method void runMe() updated to call FormFactory

public method Form getUserPreferencesConfigurationForm( NotificationConfiguration nc, TablePreferencesConfiguration tpc) to obtain a form to check for valid input. It also retrieves values of the new valid parameters and saves the settings in the preferences file, optionally after having called public method resetTablePreferences() in class PreferencesFile to reset table preferences.

9. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3498]) Refs #582. Refs #287. Update in changeset ​[3497] reverted, as one file was missing.

[olle]

(In [3499]) Refs #582. Refs #287. Basic support for storing table preferences added, but without functionality to tables:

1. Class/file core/PreferencesFile.java in api/core updated;
2. New private instance variable int tablePreferencesMode and

List<TablePreferences> tablePreferencesList with public accessor methods added.

2. Private method void fetchPreferences() updated with call

to new private method void fetchTablePreferences().

3. New private method void fetchTablePreferences() added.

It fetches user preferences for tables from user preferences file and stores them in instance variables.

4. New private convenience method

List<String> listStringToStringList(String listStr, String separator) added. It creates a string list from a list string.

5. New public method void resetTablePreferences() added.

It resets the table preferences list.

6. Public method void save() updated with call to new

private method void saveTablePreferences().

7. New private method void saveTablePreferences() added.

It saves table preferences in user preferences file.

8. New private convenience method String valueString(Object input)

added. It returns the input value as string if not null, else an empty string.

2. New class/file io/ColumnPreferences.java in api/core/ added.

It stores temporary values of preferences for a column.

3. New class/file io/TablePreferences.java in api/core/ added.

It stores temporary values of preferences for a table.

4. New class/file io/TablePreferencesConfiguration.java in

api/core/ added. It stores temporary values of configuration settings for table preferences.

5. Class/file io/NotificationConfiguration.java in api/core/

updated by removing debug output that would be undesirably long when the preferences file is used to store table preferences.

6. Class/file action/preferences/ViewPreferences.java in

client/servlet/ updated:

1. Public method void runMe() updated to obtain table

preferences configuration from the preferences file and call new FormFactory method Form getUserPreferencesConfigurationForm( NotificationConfiguration nc, TablePreferencesConfiguration tpc) to obtain a form to display.

7. Class/file gui/form/FormFactory.java in client/servlet/

updated:

1. New public method

Form getUserPreferencesConfigurationForm( NotificationConfiguration nc, TablePreferencesConfiguration tpc) added. It calls new private methods for obtaining Fieldsets for notifaction and table preferences configuration, and returns a form for user preferences configuration settings.

2. Public method

Form getNotificationConfigurationForm(NotificationConfiguration nc) changed to return a Fieldset instead of a Form, Fieldset getNotificationConfigurationFieldset(NotificationConfiguration nc)

3. New public method

Fieldset getTablePreferencesConfigurationFieldset(TablePreferencesConfiguration tpc) added. It returns a Fieldset for table preferences configuration settings.

4. New private method

Select<VInteger> getTablePreferencesModeSelectBox(int modeValue) added. It creates a select box for table preferences mode.

8. Class/file action/preferences/SavePreferences.java in

client/servlet/ updated:

1. New valid parameters VBoolean VTABLEPREFERENCESRESET and

VInteger VTABLEPREFERENCESMODE added, for obtaining values of table preferences reset flag and usage mode, respectively.

2. Public method void runMe() updated to call FormFactory

public method Form getUserPreferencesConfigurationForm( NotificationConfiguration nc, TablePreferencesConfiguration tpc) to obtain a form to check for valid input. It also retrieves values of the new valid parameters and saves the settings in the preferences file, optionally after having called public method resetTablePreferences() in class PreferencesFile to reset table preferences.

9. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In ​[3511]) English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys in connection with Ticket #635 (It should be possible to start spectrum searches from the menu).

[olle]

(In [3512]) Refs #287. Refs #635. English dictionary file locale/en/dictionary in client/servlet/ updated by changing value string for key "XTandem" from "XTandem" to the correct "X!Tandem" for menu items.

[olle]

(In [3529]) Refs #639. Refs #535. Refs #287. Hits comparison of protein lists updated with option to only use leading proteins when comparing proteins:

1. Class/file action/hit/HitsComparisonReport.java in client/servlet/

updated with new public valid parameter VBoolean VONLYUSELEADINGPROTEINS.

2. Class/file gui/form/FormFactory.java in client/servlet/ updated in

public method Form getHitsComparisonReportForm(Project project, Project project1, Project project2, String filenamePrefixDefault) by adding check-box coupled to valid parameter HitsComparisonReport.VONLYUSELEADINGPROTEINS.

3. Class/file action/hit/CreateHitsComparisonReportJob.java in

client/servlet/ updated:

1. Protected method void runMe() updated by obtaining value of

new valid VBoolean parameter HitsComparisonReport.VONLYUSELEADINGPROTEINS and setting it as values of new job parameter "onlyUseLeadingProteins".

4. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated:
5. Private inner class HitsComparisonData updated with new instance

variable boolean onlyUseLeadingProteins with public accessor methods. The default value is false.

2. Public method

void run(Request request, Response response, ProgressReporter progress) updated to obtain value of new job parameter "onlyUseLeadingProteins" and transferring it to new instance of HitsComparisonData.

3. Public method

void doExport(DbControl dc, HitsComparisonData hcd, File outCoreFile, ProgressReporter progress) updated by giving value of onlyUseLeadingProteins flag as argument when calling private method List<Hit> ofetchHitSelectionHitList(DbControl dc, Project theProject, ...). If the comparison is not of proteins, the value has first been reset to false.

4. Private method

List<Hit> fetchHitSelectionHitList(DbControl dc, Project theProject, ...) updated with new argument Boolean onlyUseLeadingProteins, that is given as argument when calling private method private ItemQuery<Hit> createBasicHitQuery(Project theProject, ...).

5. Private method

ItemQuery<Hit> createBasicHitQuery(Project theProject, ...) updated with new argument Boolean onlyUseLeadingProteins. If its value is true, the query is restricted to entries with property "firstInCombination" being equal to null.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key.

[olle]

(In [3904]) Refs #700. Refs #287. First version of support for simple search form for X!Tandem searches:

1. Class/file action/xTandemInput/ViewActiveXTandemParameterSetStorage.java

in client/servlet/ updated to support both a simple and an advanced X!Tandem search form:

1. New public static valid parameter VBoolean VXTANDEMPARAMETERSETSIMPLEFORMFLAG

added. It is used to store a flag indicating if a simple form is desired.

2. Public method void runMe() updated to retrieve the value of new valid

parameter VBoolean VXTANDEMPARAMETERSETSIMPLEFORMFLAG and set a flag variable useSimpleForm indicating if a simple form is desired. If the value of the valid parameter is null, the latter variable is set to true, as a simple form is the default. Since the value of the new valid parameter only is null the first time the action is entered for the form, the value is also used to set a boolean flag variable firstEntry. If a simple form is to be used, form class XTandemParameterSetFormSimple is used, otherwise class XTandemParameterSetForm. The first time the action is entered for a form X!Tandem data is read from the database, otherwise it is retrieved from data supplied with the form. In this case, one of two new methods named updateAdvancedFormMultipleChoiceFields(...) is called to update the multiple choice data in the current form. A new button is added to toggle the form type between simple and advanced. This button sets the value of valid parameter VXTANDEMPARAMETERSETSIMPLEFORMFLAG to force a change of form type when the action is re-entered.

3. New private method

XTandemParameterSetForm updateAdvancedFormMultipleChoiceFields(XTandemParameterSetForm form) added. It updates advanced form multiple choice fields.

4. New private method

XTandemParameterSetFormSimple updateAdvancedFormMultipleChoiceFields(XTandemParameterSetFormSimple form) added. It updates simple form multiple choice fields.

5. New private convenience method

List<String> fetchValidStringList(String quantityName, VString param) added. It fetches a string list from for a VString valid parameter from the HTTP request.

2. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3933]) Refs #547. Refs #287. First version of limited number of items in the "Select Project" menu in Proteios SE:

1. New class/file action/DummyAction.java in client/servlet/ added.

It does nothing, and returns directly. It is Intended to be used for action links in menus, where one wants a menu item with a comment but no action, but does not want the action link to be disabled, as this would make the entry to be dimmed, and hard to read.

2. Class/file gui/MainMenu.java in client/servlet/ updated:
3. New private constant final int MAX_NUM_PROJECT_ITEMS added.

Its value is set to 20.

2. Private method Node createSelectProjectNode() updated to limit

the number of displayed project items to the set limit. If the number of projects is larger, the list will be truncated, and an ellipsis item, a separator, and a new "more projects" item added. However, if the active project is not among the projects listed by default, it will be inserted after the ellipsis item and the separator, while the last project item is the default list will be omitted. The "more projects" item will display the number of projects not listed, e.g. "6 more" if 6 more projects exist. Clicking on the "more projects" menu will redirect the user to a listing of all available projects.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

[olle]

(In [3952]) Refs #704. Refs #585. Refs #287. Project table tool bar updated to remove the "Delete" button coupled to action DeleteItems, and rename button "Trash Project" coupled to action TrashProject to new name "Delete":

1. Class/file action/project/ListMyProjects.java in client/servlet/

updated:

1. Public method void runMe() updated to remove the "Delete" button

coupled to action DeleteItems from the tool bar of the project table.

2. Class/file gui/Toolbar.java in client/servlet/ updated:

a Public method void clear() updated to first check if instance variable ArrayList<AbstractLink> toolbar differs from null, before calling its clear() method.

3. English dictionary file locale/en/dictionary in client/servlet/

updated by changing the string value for key TrashProject from "Trash Project" to "Delete".

[olle]

(In [3989]) Refs #707. Refs #287. Refs #290. First version of support for editing of Mascot parameter set storage properties:

1. New class/file action/mascot/ViewMascotParameterSetStorageProperties.java

in client/servlet/ added. It implements interface ContextEnabled and adds a "Properties" button to the tool bar of tables listing MascotParameterSetStorage items. It is checked that exactly one item is selected, and its id is set to value of new valid parameter Vinteger VMASCOTPARAMETERSETSTORAGEID in new class ViewActiveMascotParameterSetStorageProperties, after which action is forwarded to the latter class.

2. New class/file action/mascot/ViewActiveMascotParameterSetStorageProperties.java

in client/servlet added. It obtains the value of new valid parameter Vinteger VMASCOTPARAMETERSETSTORAGEID, and gets the corresponding MascotParameterSetStorage item, whose properties are shown using new form MascotParameterSetStoragePropertiesForm. A "Save" button is coupled to action link to new class SaveMascotParameterSetStorageProperties.

3. New class/file gui/form/MascotParameterSetStoragePropertiesForm.java

in client/servlet/ added. It creates a form for properties of a MascotParameterSetStorage item.

4. New class/file action/mascot/SaveMascotParameterSetStorageProperties.java

in client/servlet/ added. It obtains values from the MascotParameterSetStoragePropertiesForm form and saves them in the corresponding MascotParameterSetStorage item.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

6. Default icon settings file "default" in icons/ in client/servlet/

updated with new icon assignments.

[olle]

(In [3992]) Refs #707. Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new and updated string keys for Mascot parameter sets, in order to get better consistency with form for other search parameter sets.

[olle]

(In ​[3997]) Refs #707. Refs #471. First version of support for editing of OMSSA parameter set storage properties:

1. New class/file action/omssa/ViewOMSSAParameterSetStorageProperties.java

in client/servlet/ added. It implements interface ContextEnabled and adds a "Properties" button to the tool bar of tables listing OMSSAParameterSetStorage items. It is checked that exactly one item is selected, and its id is set to value of new valid parameter Vinteger VOMSSAPARAMETERSETSTORAGEID in new class ViewActiveOMSSAParameterSetStorageProperties, after which action is forwarded to the latter class.

2. New class/file action/omssa/ViewActiveOMSSAParameterSetStorageProperties.java

in client/servlet added. It obtains the value of new valid parameter Vinteger VOMSSAPARAMETERSETSTORAGEID, and gets the corresponding OMSSAParameterSetStorage item, whose properties are shown using new form OMSSAParameterSetStoragePropertiesForm. A "Save" button is coupled to action link to new class SaveOMSSAParameterSetStorageProperties.

3. New class/file gui/form/OMSSAParameterSetStoragePropertiesForm.java

in client/servlet/ added. It creates a form for properties of an OMSSAParameterSetStorage item.

4. New class/file action/omssa/SaveOMSSAParameterSetStorageProperties.java

in client/servlet/ added. It obtains values from the OMSSAParameterSetStoragePropertiesForm form and saves them in the corresponding OMSSAParameterSetStorage item.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

[olle]

(In [3998]) Refs #707. Refs #362. Refs #287. First version of support for editing of X!Tandem parameter set storage properties:

1. New class/file action/xTandemInput/ViewXTandemParameterSetStorageProperties.java

in client/servlet/ added. It implements interface ContextEnabled and adds a "Properties" button to the tool bar of tables listing XTandemParameterSetStorage items. It is checked that exactly one item is selected, and its id is set to value of new valid parameter Vinteger VXTANDEMPARAMETERSETSTORAGEID in new class ViewActiveXTandemParameterSetStorageProperties, after which action is forwarded to the latter class.

2. New class/file action/xTandemInput/ViewActiveXTandemParameterSetStorageProperties.java

in client/servlet added. It obtains the value of new valid parameter Vinteger VXTANDEMPARAMETERSETSTORAGEID, and gets the corresponding XTandemParameterSetStorage item, whose properties are shown using new form XTandemParameterSetStoragePropertiesForm. A "Save" button is coupled to action link to new class SaveXTandemParameterSetStorageProperties.

3. New class/file gui/form/XTandemParameterSetStoragePropertiesForm.java

in client/servlet/ added. It creates a form for properties of a XTandemParameterSetStorage item.

4. New class/file action/xTandemInput/SaveXTandemParameterSetStorageProperties.java

in client/servlet/ added. It obtains values from the XTandemParameterSetStoragePropertiesForm form and saves them in the corresponding XTandemParameterSetStorage item.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

[olle]

(In [4016]) Refs #717. Refs #287. Refs #290. First version of extensions button for hits report table:

1. New class/file HitContext?.java in client/servlet added.

It is based on class DirectoryContext, but has an attribute int order, in analogy with class TableToolbarContext.

2. Class/file gui/MainMenu.java in client/servlet/ updated;
3. New private method

Node listNode(Class<?> wrapper, Class<?> data, String dictionaryKey, Boolean inproject, Class<?> forwardClass) added.

2. Private method

Node listNode(Class<?> wrapper, Class<?> data, String dictionaryKey, Boolean inproject) updated by callinig new method Node listNode(Class<?> wrapper, Class<?> data, String dictionaryKey, Boolean inproject, Class<?> forwardClass) with argument forwardClass set to ShowTable.class, which results in the same behavior as previously.

3. Public method Node createHitsReportN() updated by creating

the node by calling new method Node listNode(Class<?> wrapper, Class<?> data, String dictionaryKey, Boolean inproject, Class<?> forwardClass) with argument forwardClass set to new class ListHits.class.

3. Class/file gui/GUIFactory.java in client/servlet/ updated:
4. New public method

ActionLink getListLink(Class<?> wrapper, Class<?> data, String dictionaryKey, Boolean inproject, Class<?> forwardClass) added.

2. Public method

ActionLink getListLink(Class<?> wrapper, Class<?> data, String dictionaryKey, Boolean inproject) updated by calling new method ActionLink getListLink(Class<?> wrapper, Class<?> data, String dictionaryKey, Boolean inproject, Class<?> forwardClass) with argument forwardClass set to ShowTable.class, which results in the same behavior as previously.

4. Class/file action/project/ViewProjectHome.java in client/servlet/

updated:

1. Public method void runMe() updated by creating

the hits resport link by calling new GUIFactory method ActionLink getListLink(Class<?> wrapper, Class<?> data, String dictionaryKey, Boolean inproject, Class<?> forwardClass) with argument forwardClass set to new class ListHits.class.

5. New class/file action/hit/ListHits.java in client/servlet/

added. It is based on class ShowTable, but adds a hits extensions button to the toolbar. Extension classes are sorted depending on the values of their HitContext order attribute before being added to the extensions list.

6. Following classes/files in client/servlet/ were updated to

implement ContextEnabled through the new class HitContext, instead of TableToolbarContext for tables of class Hit:

1. action/hit/CombineHitsStep1.java
2. action/hit/ProteinAssembly1.java
3. action/hit/PrideExport.java
4. action/hit/HitsComparisonReportStep1.java
5. action/hit/ExclusionList.java

7. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

8. Default icon settings file "default" in icons/ in client/servlet/

updated with new icon assignments.

[olle]

(In [4040]) Refs #720. Refs #554. Refs #287. Refs #290. First version of file type extensions button for file properties form:

1. New class/file FileTypeContext.java in client/servlet/ added.

It is based on class HitContext, but has an attribute String fileTypeString, defining the file type for the context.

2. Class/file action/file/ViewActiveFile.java in client/servlet/

updated:

1. Public method void runMe() updated by exchanging code connected

to adding an "Original search results" button for a call to new private method Form addFileTypeExtensionsButton(Form form, File file), that adds a file type extension button.

2. New private method Form addFileTypeExtensionsButton(Form form, File file)

added. It adds a file type extensions button to the toolbar, with a pop-up link to a table with extension classes implementing interface ContextEnabled through new class FileTypeContext, where the context file type attribute value equals that of the current file item.

3. Class/file action/file/ViewOriginalMascotResultsExtension.java

in client/servlet/ updated to implement ContextEnabled through the new class FileTypeContext for file type string FileType.MASCOT_XML.

4. Class/file action/file/ViewOriginalXTandemResultsExtension.java

in client/servlet/ updated to implement ContextEnabled through the new class FileTypeContext for file type string FileType.TANDEM_RESULT.

5. English dictionary file locale/en/dictionary in client/servlet/

updated with new string keys.

6. Default icon settings file "default" in icons/ in client/servlet/

updated with new icon assignments.

[olle]

(In [4050]) Refs #706. Refs #287. Refs #290. Hits table "Clear Hits" button funstionality updated to allow only hits with selected properties (external gel id or local sample id) to be erased:

1. Class/file action/hit/ClearHits.java in client/servlet/ updated by commenting out the line stating that the class implements ContextEnabled, thereby effectively inactivating the class, as no button will be created for it. It is replaced by new class ClearSpecialHitsStep1.

2. New class/file action/hit/ClearSpecialHitsStep1.java in client/servlet/ added. It implements ContextEnabled through class TableToolbarContext for the Hits table. It displays a form created by new class ClearSpecialHitsForm together with a help text, and a button coupled to ab action link to new class ClearSpecialHits.

3. New class/file gui/form/ClearSpecialHitsForm.java in client/servlet/ added. Depending on the projects type, it contains a select box for gel id or local sanple id. The select boxes are extended with an option for "All in project".

4. New class/file action/hit/ClearSpecialHits.java added. It retrieves data from valid parameters VString ExternalGelIdField.VPARAM and VString LocalSampleSelect.VPARAM, and removes selected hits.

5. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

6. Default icon settings file "default" in icons/ in client/servlet/ updated with new icon assignments.

[olle]

(In [4053]) Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4060]) Refs #287. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4073]) Refs #668. Refs #287. First version of support for running msInspect feature finding from Proteios SE:

1. New class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ added. It implements interface ContextEnabled through class FileContext. List of id values for selected spectrum files are added as hidden fields to the form, and a button is displayed that is coupled to an action link to new class RunMsInspect.

2. New class/file action/msInspect/RunMsInspect.java in client/servlet/ added. It retrieves a list of id values for spectrum files from valid parameter VInteger VSPECTRUMFILEID and settings from msInspect properties file msinspect.properties, after which it creates one job for each spectrum file managed by new plug-in class RunMsInspectPlugin.

3. New class/file plugins/RunMsInspectPlugin.java in plugin/ added. It copies the spectrum input file to a temporary file with a time stamp in the file name to the temp folder, and then ruins the msInspect program on the latter file. It attempts to upload the result file, after which it deletes the created temporary files (if uploading the result file was unsuccessful, this file is kept for manual upload).

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4082]) Refs #668. Refs #287. the following classes/files were updated to refer to processing with msInspect program as "feature detection" in displayed text:

1. action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/.

2. action/msInspect/RunMsInspect.java in client/servlet/.

3. plugins/RunMsInspectPlugin.java in plugin/.

4. locale/en/dictionary in client/servlet/.

[olle]

(In [4089]) Refs #668. Refs #287. Support for running msInspect feature detection from Proteios SE updated to allow user selected strategy option:

1. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated by adding a menu select box for selecting a strategy option. The option string parameter is coupled to new valid parameter VString RunMsInspect.VMSINSPECTSTRATEGY. The default option is marked "default", and corresponds to no strategy option being used.

2. Class/file action/msInspect/RunMsInspect.java in client/servlet/ updated to retrieve the string from new valid parameter VString VMSINSPECTSTRATEGY and transferring it as a job parameter to plug-in class RunMsInspectPlugin.

3. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated to retrieve the strategy string from the job parameter. If the string is null or an empty string (corresponding to the default option), no changes are made to the msInspect command line. Otherwise, the retrieved string is used as value for an extra option --strategy=value in the msInspect command line.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

(In [4097]) Refs #730. Refs #535. Refs #287. Hits Comparison Report updated in GUI, to hopefully be simpler and increase consistency:

1. Class/file action/hit/HitsComparisonReportStep1.java in client/servlet/ updated in page title.

2. Class/file action/hit/HitsComparisonReport.java in client/servlet/ updated in page title.

3. Class/file gui/form/ProjectComparisonForm.java in client/servlet/ updated to use one fieldset for each hit selection, when selecting projects, as separate fieldsets are used when selecting filter settings.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4099]) Refs #737. Refs #535. Refs #287. Hits comparison report updated with new option to include modifications when comparing peptides:

1. Class/file action/hit/HitsComparisonReport.java in client/servlet/ updated with new public static valid parameter VBoolean VINCLUDEMODIFICATIONS.

2. Class/file gui/form/HitComparisonForm.java in client/servlet/ updated by adding new fieldset for peptide comparisons only and adding a new check box coupled to valid parameter HitsComparisonReport.VINCLUDEMODIFICATIONS to it. Default setting for including modifications is false. Code for hidden forward field moved to after visible fields.

3. Class/file action/hit/CreateHitsComparisonReportJob.java in client/servlet/ updated to obtain value of new valid parameter VBoolean HitsComparisonReport.VINCLUDEMODIFICATIONS and set the value to new job parameter (value equal to null are set to false, which is the default value).

4. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated to obtain the value of new job parameter for the include modifications flag. Private inner class HitsComparisonData updated with new private instance variable boolean modificationsIncluded with public accessor methods, and the value of the new boolean variable is set to that of the new job parameter for including modifications. Private method String fetchCompareString(Hit hit, boolean gelBasedComparison, String comparisonType) updated with new argument Boolean modificationsIncluded, and the full description/sequence string is used for comparisons when the value of modificationsIncluded is true, otherwise the string up to the first space is used.

5. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4102]) Refs #736. Refs #535. Refs #287. Hits comparison report updated in GUI by placing general selections on first selection page, and display relevant options on second selection page, based on the initial selections. Option to select quantitative comparison report added, but no functionality for this alternative added:

1. Class/file action/hit/HitsComparisonReportStep1.java in client/servlet/ updated in instruction text.

2. Class/file gui/form/HitComparisonStep1Form.java in client/servlet/ updated by adding new initial fieldset for selecting general hits comparison settings.

3. Class/file action/hit/HitsComparisonReport.java in client/servlet/ updated. New valid parameter VBoolean VQUANTITATIVECOMPARISONREPORT added. Protected method void runMe() updated to retrieve values of general hits comparison settings from valid parameters and transfer them to form class HitComparisonForm. Instruction text updated.

4. Class/file gui/form/HitComparisonForm.java in client/servlet/ updated by adding arguments Boolean quantitativeComparison and String comparisonType to constructor. GUI updated by addition of new initial fieldset reporting values of general hits comparison settings, and only displaying relevant options, based on the initial selections.

5. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4105]) Refs #736. Refs #535. Refs #287. First preliminary version of hits comparison report with support for quantitative comparison report:

1. Class/file action/hit/HitsComparisonReport.java in client/servlet/ updated by addition of new valid parameters VString VQUANTITYVARIABLE and VString VQUANTITYENTRY. Displayed instruction text is now modified depending on whether a non-quantitative or quantitative comparison report should be created.

2. Class/file gui/form/HitComparisonForm.java in client/servlet/ updated to display different option depending on whether a non-quantitative or quantitative comparison report should be created. Selection of gel external id for the two hit selections is not available for quantitative comparison report. New private convenience method Select<VString> fillStringMultiSelectionBox(Select<VString> selectBox, List<String> optionStringList, String optionVariableName) added to simplify to create string multi-selection boxes.

3. Class/file action/hit/CreateHitsComparisonReportJob.java in client/servlet/ updated to support quantitative comparison report. Input data consistency checks modified depending on whether a non-quantitative or quantitative comparison report should be created. Values of new valid parameters HitsComparisonReport.VQUANTITYVARIABLE and HitsComparisonReport.VQUANTITYENTRY are retrieved from request and transfered to the job by new job parameters. Different plug-in classes are used for the created job depending on whether a non-quantitative or quantitative comparison report should be created (HitsComparisonReportPlugin for non-quantitative and new plug-in class HitsComparisonQuantitativeReportPlugin for quantitative). New key strings needed for quantitative comparison report added to list used to obtain localized strings used by the plug-in.

4. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated by removal of unused private instance variable boolean gelBasedExport and related public accessor methods.

5. New class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ added. It is based on existing class HitsComparisonReportPlugin, but modified for quantitative comparison report. Hit selection and report generation completely re-written. Unused methods from class HitsComparisonReportPlugin kept in code for now, in case they should be needed later.

6. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4110]) Refs #736. Refs #535. Refs #287. Quantitative comparison report updated by clarification of table header titles, addition of a column after each quantity value column for a local sample id showing the number of entries used to obtain the value, simplification of statistical calculations by omitting use of dummy values when values are missing, and use of ratio entry "+" in case values exist for hit selection 1 but not for hit selection 2, and "-" if it is the other way around:

1. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated:
   a. Addition of string constants for string selection values, in order to avoid risk of wrong functionality due to misspellings in the source code (provided the constants themselves are given the correct values :)).
   b. Table header titles have been clarified.
   c. Private method Double processHitValue(Hit hit, Double columnValue, String quantityVariable, String quantityEntry) exchanged for new private methods, Double fetchHitQuantityValue(Hit hit, String quantityVariable) and Double updateColumnValue(Double columnValue, Double newValue, String quantityEntry), that together give the same functionality, but in addition allow the number of valid quantity values to be counted for a local sample id, which is reported in a new column after the column with the quantity value.
   d. Simplification of statistical calculations by omitting use of dummy values when values are missing (meaning that there is no need for variables statisticsNullValue and nullvalue). The ratio calculations are now performed using the Apache statistics library objects ssa and ssb.
   e. Ratio presentation updated to show entry "+" in case values exist for hit selection 1 but not for hit selection 2, and "-" if it is the other way around.

2. Class/file action/hit/CreateHitsComparisonReportJob.java in client/servlet/ updated by addition of new string keys to list used to obtain localized strings used by the plug-in.

3. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4117]) Refs #739. Refs #287. File properties form updated in functionality for opening a file in the browser, provided that the MIME-type of the file is supported. A confirmation dialog is displayed before opening a file in the browser, if the file size is larger than a lower limit, but smaller than an upper limit. If the file size is larger than the upper limit, the functionality to open the file in the browser is disabled, even if the MIME-type is supported. If the file size is smaller than the lower limit and the MIME-type supported, it will as before be possible to open the file in the browser without a confirmation dialog.

1. Class/file action/file/ViewActiveFile.java in client/servlet/ updated:
   a. Two new private constants defined, long MAX_FILE_SIZE_IN_BYTES_WITHOUT_CONFIRM set to 2*1024*1024 (2 Mb), and long MAX_FILE_SIZE_IN_BYTES_FOR_SHOWING set to 10*1024*1024 (10 Mb).
   b. Public method void runMe() updated to call new public method TitledWindow createPermissionForm(Boolean recursive, int fileId, long fileSizeInBytes) to create a confirmation dialog before opening a file in the browser, if the size of the file is larger than MAX_FILE_SIZE_IN_BYTES_WITHOUT_CONFIRM, but smaller than MAX_FILE_SIZE_IN_BYTES_FOR_SHOWING. If a confirmation dialog is created, the popup link to it will replace the action link coupled to the "View" button in the toolbar. If the size of the file is larger than MAX_FILE_SIZE_IN_BYTES_FOR_SHOWING, the action link coupled to the "View" button is disabled, and an information box consisting of a titled window with an explanation for the disabled functionality is added to the row container in which the main properties form is added.
   c. New public method TitledWindow createPermissionForm(Boolean recursive, int fileId, long fileSizeInBytes) added. It creates a confirmation dialog for opening a large file, with a "Yes" button coupled to an action link equal to the one normally coupled to the "View" button in the main toolbar, except for the label.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key.

[olle]

(In [4122]) Refs #740. Refs #392. Refs #287. Non gel-based hits import updated with support for obtaining local sample id from BioMaterial associated with peaklist file:

1. Class/file action/hit/ImportHitsNonGelWizard.java in client/servlet/ updated:
   a. New text info box added.
   b. Form obtained from new class ImportHitsNonGelWizardStep1EntryModeForm.
   c. Link for "Next" button changed to action link to new class ImportHitsNonGelWizardStep1AdditionalParameters.

2. New class/file gui/form/ImportHitsNonGelWizardStep1EntryModeForm.java in client/servlet/ added. It calls new class LocalSampleIdEntryModeMenu to display a menu to select local sample id input method from.

3. New class/file gui/form/LocalSampleIdEntryModeMenu.java in client/servlet/ added. It creates a menu for selecting local sample id input method. The value is stored in new valid parameter VSTRING LocalSampleIdEntryModeMenu.VPARAM. Default is "Enter explicitly", as previously used.

4. New class/file action/hit/ImportHitsNonGelWizardStep1AdditionalParameters.java in client/servlet/ added. It displays a text info box with text and displays options for selecting additional parameters, adapted to previously made choices. Link for "Next" button is coupled to action link to class ImportHitsNonGelWizardStep1a.

5. Class/file gui/form/ImportHitsNonGelWizardStep1Form.java in client/servlet/ updated:
   a. New constructor which takes extra argument String localSampleIdEntryMode added.
   b. It displays an initial field set that reports the selected setting for local sample id input.
   c. Input fields for local sample id are only shown if explicit entry of this parameter has been selected.

6. Class/file action/hit/ImportHitsNonGelWizardStep1a.java in client/servlet/ updated:
   a. It obtains value of valid parameter VSTRING LocalSampleIdEntryModeMenu.VPARAM and saves it as a session parameter.
   b. It only checks and transfers a local sample id value if the latter has been chosen to be explicitly entered.

7. Class/file action/hit/ImportHitsNonGelWizardStep1b.java in client/servlet/ updated to transfer value of valid parameter VSTRING LocalSampleIdEntryModeMenu.VPARAM to created job as job parameter.

8. Class/file plugins/PeakListToHitNonGelPlugin.java in plugin/ updated:
   a. Value of local sample id entry mode obtained from new job parameter.
   b. Local sample id is obtained from bio material associated with the peaklist file, if this option has been selected. In this case, an attempt is made to obtain fraction id from an annotation for the peaklist file, with annotation type name "fraction". If this attempt fails, an attempt is made to obtain fraction id from the peaklist filename through use of a regular expression pattern, if this option has been chosen.

9. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In [4126]) Refs #740. Refs #392. Refs #287. Non gel-based hits import updated to make options for obtaining optional fraction id independent of the way local sample id is obtained:

1. Class/file action/hit/ImportHitsNonGelWizardStep1AdditionalParameters.java in client/servlet/ updated in info box text.

2. Class/file gui/form/ImportHitsNonGelWizardStep1Form.java in client/servlet/ updated to display a pop-up menu for selecting method to obtain fraction id instead of a checkbox for obtaining fraction id using a regex pattern on the peaklist filename (this is now one of the available options). The pop-up menu is obtained from new class FractionIdEntryModeMenu.

3. Class/file gui/form/client/servlet/src/org/proteios/gui/form/FractionIdEntryModeMenu.java in client/servlet/ added. It creates a pop-up menu for selecting method to obtain fraction id.

4. Class/file action/hit/ImportHitsNonGelWizardStep1a.java in client/servlet/ updated to obtain value of new valid parameter VSTRING FractionIdEntryModeMenu.VPARAM from request and save it to session.

5. Class/file action/hit/ImportHitsNonGelWizardStep1b.java in client/servlet/ updated to obtain value of new valid parameter VSTRING FractionIdEntryModeMenu.VPARAM from session and transfer it to created job as job parameter.

6. Class/file plugins/PeakListToHitNonGelPlugin.java in plugin/ updated:
   a. Value of string defining method to obtain fraction id value obtained from job parameter and used to decide how the fraction id is obtained.
   b. New private convenience method String fetchFractionIdFromFileAnnotation(DbControl dc, File file) added. It attempts to obtain fraction id from file annotation "fraction".

7. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In [4148]) Refs #744. Refs #287. First version of support for running OpenMS feature finding from Proteios SE (progress report not supported):

1. New class/file action/file/UseSpectrumFileForOpenMsSearchExtension.java in client/servlet/ added. It implements interface ContextEnabled through class FileContext. List of id values for selected spectrum files are added as hidden fields to the form, and a button is displayed that is coupled to an action link to new class RunOpenMs.

2. New class/file action/openMs/RunOpenMs.java in client/servlet/ added. It retrieves a list of id values for spectrum files from valid parameter VInteger VSPECTRUMFILEID and settings from OpenMS properties file openms.properties, after which it creates one job for each spectrum file managed by new plug-in class RunOpenMsPlugin. If OpenMS programs PeakPicker and FeatureFinder should be run in a pipeline, a second job is created that uses the result file from the first job as input file.

3. New class/file plugins/RunOpenMsPlugin.java in plugin/ added. It copies the spectrum input file to a temporary file with a time stamp in the file name to the temp folder, and then ruins the OpenMS program on the latter file. It attempts to upload the result file, after which it deletes the created temporary files. The result file will not be deleted if it is to be used as input for another program in a pipeline, or if uploading the result file to Proteios SE was unsuccessful.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4154]) Refs #740. Refs #392. Refs #287. Non gel-based hits import updated to display an error message if no peaklist files are selected:

1. Class/file action/hit/ImportHitsNonGelWizardStep1b.java in client/servlet/ updated in protected method void runMe() to display an error message if no peaklist files are selected.

[olle]

(In [4169]) Refs #582. Refs #287. Pop-up menu label "Use table preferences:" exchanged for "Save table preferences:", in order to make the meaning clearer:

1. English dictionary file locale/en/dictionary in client/servlet/ updated in entry for string key.

[olle]

(In [4175]) Refs #749. Refs #668. Refs #744. Refs #356. Refs #287. First version of support for starting feature detection from the menu:

1. Class/file gui/MainMenu.java in client/servlet/ updated:
   a. Private method Node createProjectMenu() updated by adding cascade menu for performing feature detection.

2. New class/file action/file/PerformMsInspectSearch.java in client/servlet/ added. It displays the file selection form and then forwards the action to class UseSpectrumFileForMsInspectSearchExtension.

3. New class/file action/file/PerformOpenMsSearch.java in client/servlet/ added. It displays the file selection form and then forwards the action to class UseSpectrumFileForOpenMsSearchExtension.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In [4188]) Refs #752. Refs #668. Refs #614. Refs #287. Support for running msInspect feature detection from Proteios SE updated with option to import the created feature file directly:

1. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated with new check box for option to import created feature file. The check box is coupled to new valid parameter VBoolean RunMsInspect.VMSINSPECTIMPORTRESULTS. Default is to not import the feature file directly.

2. Class/file action/msInspect/RunMsInspect.java in client/servlet/ updated:
   a. New valid parameter VBoolean VMSINSPECTIMPORTRESULTS added.
   b. Protected method void runMe() updated to retrieve the value of valid parameter VBoolean VMSINSPECTIMPORTRESULTS, and if the value is true create an import job after the feature detection job. The path of the feature file to be created is transferred to the import job as a string job parameter. Jobs are created by calling new private methods Job createMsInspectJob(...) and Job createMsInspectImportJob(...).
   c. New private method Job createMsInspectJob(DbControl dc, File spectrumFile, ... , Job blockerJob) added. It creates an msInspect job.
   d. New private method Job createMsInspectImportJob(DbControl dc, String featureFilePathStr, String featureFileName, Job blockerJob) added. It creates an msInspect import job.

3. Class/file plugins/MsInspectFeatureImporter.java in plugin/ updated:{{BR]]a. Public method void run(Request request, Response response, ProgressReporter progress) updated to retrieve value of feature file path from a string job parameter and obtain the feature file from this, in case the File value retrieved from a File job parameter is null.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4206]) Refs #751. Refs #744. Refs #614. Refs #287. Support for running OpenMS feature detection from Proteios SE updated with option to import the created feature file directly:

1. Class/file action/file/UseSpectrumFileForOpenMsSearchExtension.java in client/servlet/ updated with new check box for option to import created feature file. The check box is coupled to new valid parameter VBoolean RunOpenMs.VOPENMSIMPORTRESULTS. Default is to not import the feature file directly.

2. Class/file action/openMs/RunOpenMs.java in client/servlet/ updated:
   a. New valid parameter VBoolean VOPENMSIMPORTRESULTS added.
   b. Protected method void runMe() updated to retrieve the value of valid parameter VBoolean VOPENMSIMPORTRESULTS, and if the value is true create an import job after the feature detection job. As import of features requires a preceding feature detection job, the code for running a single OpenMS job has been updated to clarify if the job instance is a PeakPicker or FeatureFinder job. The path of the feature file to be created is transferred to the import job as a string job parameter. Import jobs are created by calling new private method Job createOpenMsImportJob(...).
   c. New private method Job createOpenMsImportJob(DbControl dc, String featureFilePathStr, String featureFileName, Job blockerJob) added. It creates an OpenMS import job.

3. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4211]) Refs #761. Refs #751. Refs #744. Refs #287. Main form for running OpenMS feature detection from Proteios SE updated in main form by placing options in different sections, depending on what program the options control:

1. Class/file action/file/UseSpectrumFileForOpenMsSearchExtension.java in client/servlet/ updated in protected method void runMe() by introducing separate sections in main form for general options, PeakPicker options, and FeatureFinder options.

2. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4213]) Refs #761. Refs #744. Refs #287. First version of support for new OpenMS FeatureFinder options for algorithm "centroided":

1. Class/file action/file/UseSpectrumFileForOpenMsSearchExtension.java in client/servlet/ updated:
   a. Protected method void runMe() updated to add input fields for the new OpenMS options in the OpenMS form. The input fields are coupled to new valid parameters in class RunOpenMs.

2. Class/file action/openMs/RunOpenMs.java in client/servlet/ updated:
   a. New valid parameters added for the OpenMS options to be supported, together with constants for default values of the new parameters.
   b. Protected method void runMe() updated to obtain values of new options from valid parameters and transfer them to private method Job createOpenMsJob(DbControl dc, ...) in new arguments.
   c. Private method Job createOpenMsJob(DbControl dc, ...) updated with new arguments for the OpenMS options to support. The parameter values are transferred to the created job as job parameters.

3. Class/file plugins/RunOpenMsPlugin.java in plugin/ updated:
   a. Private method void execute(Request request, Response response, ProgressReporter progress) updated to obtain values of new parameters from job parameters and transfer them to private method void openMsSearchLocal(...).
   b. Private method void openMsSearchLocal(...) updated with arguments for new parameters and variables. It calls new private method String createOpenMsIniFile(...) to create an optional temporary OpenMS INI file. If an INI file is created, it is given as input option on the command line when starting the OpenMS program.
   c. New private method String createOpenMsIniFile(...) added. It calls new private method void updateTextFile(...) to adapt a copy of new OpenMS INI template file openms_featurefinder_centroided_ini_file_template.ini to include values of given OpenMS program parameter values.
   d. New private method void updateTextFile(String sourceFileURLStr, String targetDir, String targetFile, List<String> stringReplaceList) added. It updates a copy of a file on the server file system by replacing key strings with new text.
   e. New private convenience method void writeLine(FileWriter fw, String string) added to support creation of text files. Various instance variables with accessor methods also added to support this task.

4. New OpenMS INI template file content/openms_featurefinder_centroided_ini_file_template.ini in client/servlet/ added. It contains an OpenMS INI file for running FeatureFinder with algorithm "centroided", but with values for selected parameters exchanged for unique text markers.

5. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

(In [4234]) Refs #763. Refs #534. Refs #287. Refs #290. Support of running Mascot searches from Proteios SE updated by option to import results automatically:

1. Class/file action/mascot/SelectMascotParameterSetStorage.java in client/servlet/ updated to add new button to create search job and import results. The selected button should be identified by the value of new valid parameter VBoolean SearchMascot.VMASCOTIMPORTRESULTSFLAG being set to true.

2. Class/file gui/form/MascotStorageForm.java in client/servlet/ updated by extendng the form with a new field set "Mascot - Additional Options not in Parameter Set", with initially a single check box "Import results", coupled to new valid parameter VBoolean SearchMascot.VMASCOTIMPORTRESULTSFLAG. The check box should as default not be checked.

3. Class/file action/mascot/SaveMascotParameterSetStorage.java in client/servlet/ updated to retrieve the value of new valid parameter VBoolean SearchMascot.VMASCOTIMPORTRESULTSFLAG and add it as parameter to the forward action link, using the same valid parameter. This ensures that the value is transferred to the action creating the search job after the parameters have been saved.

4. Class/file action/mascot/SearchMascot.java in client/servlet/ updated to retrieve the value of new valid parameter VBoolean SearchMascot.VMASCOTIMPORTRESULTSFLAG and transfer it as job parameter to the created search job.

5. Class/file plugins/SearchMascotPlugin.java in plugin/ updated:
   a. Private method void execute(Request request, Response response, ProgressReporter progress) updated to retrieve value of Boolean results import flag from job parameter, and use it as argument when calling updated private method void mascotSearchViaWebInterface(..., Boolean importResultsFlag).
   b. Private method void mascotSearchViaWebInterface(...) updated with new argument Boolean importResultsFlag. If the value is true, new private method Job createImportJob(String pluginClassName, String jobName, File inputFile) is called to create an import job to import the results. Job done message updated with info regarding uploaded file and optionally created import job.
   c. Private method void mascotResultExportViaWebInterface(...) updated to File mascotResultExportViaWebInterface(...) and return the uploaded results file item obtainded from private method File uploadFileViaWebInterface(PostMethod(...).
   d. Private method void uploadFileViaWebInterface(PostMethod(...) updated to File uploadFileViaWebInterface(PostMethod(...) and return the uploaded results file item.
   e. New private method Job createImportJob(String pluginClassName, String jobName, File inputFile) added. It creates an import job to import results.

6. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

7. Default icon settings file "default" in icons/ in client/servlet/ updated with icon assignments for new string keys.

[olle]

(In [4238]) Refs #763. Refs #362. Refs #287. Refs #290. Support of running X!Tandem searches from Proteios SE updated by option to import results automatically:

1. Class/file action/file/UseSpectrumFileForXTandemSearchExtension.java in client/servlet/ updated to add new button to create search job and import results. The selected button should be identified by the value of new valid parameter VBoolean SearchXTandem.VXTANDEMIMPORTRESULTSFLAG being set to true.

2. Class/file action/xTandemInput/ViewActiveXTandemParameterSetStorage.java in client/servlet/ updated to extend the form for inspecting/editing parameters when spectrum files have been selected for searching, in which case a new field set "X!Tandem - Additional Options not in Parameter Set" will be added, with initially a single check box "Import results", coupled to new valid parameter VBoolean SearchXTandem.VXTANDEMIMPORTRESULTSFLAG. The check box should as default not be checked.

3. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java in client/servlet/ updated to retrieve the value of new valid parameter VBoolean SearchXTandem.VXTANDEMIMPORTRESULTSFLAG and add it as parameter to the forward action link, using the same valid parameter. This ensures that the value is transferred to the action creating the search job after the parameters have been saved.

4. Class/file action/xTandemInput/SearchXTandem.java in client/servlet/ updated to retrieve the value of new valid parameter VBoolean SearchXTandem.VXTANDEMIMPORTRESULTSFLAG and transfer it as job parameter to the created search job.

5. Class/file plugins/SearchXTandemPlugin.java in plugin/ updated:
   a. Private method void execute(Request request, Response response, ProgressReporter progress) updated to retrieve value of Boolean results import flag from job parameter, and use it as argument when calling updated private method void xTandemSearchViaWebInterface(..., Boolean importResultsFlag) or void xTandemSearchLocal(..., Boolean importResultsFlag).
   b. Private method void xTandemSearchViaWebInterface(...) updated with new argument Boolean importResultsFlag. If the value is true, new private method Job createImportJob(String pluginClassName, String jobName, File inputFile) is called to create an import job to import the results. Job done message updated with info regarding uploaded file and optionally created import job.
   c. Private method void xTandemSearchLocal(...) updated with new argument Boolean importResultsFlag. If the value is true, new private method Job createImportJob(String pluginClassName, String jobName, File inputFile) is called to create an import job to import the results. Job done message updated with info regarding uploaded file and optionally created import job.
   d. Private method void uploadFileViaWebInterface(...) updated to File uploadFileViaWebInterface(...) and return the uploaded results file item.
   e. Private method void uploadXTandemOutputFile(...) updated to File uploadXTandemOutputFile(...) and return the uploaded results file item.
   f. New private method Job createImportJob(String pluginClassName, String jobName, File inputFile) added. It creates an import job to import results.

6. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

7. Default icon settings file "default" in icons/ in client/servlet/ updated with icon assignments for new string keys.

[olle]

(In [4239]) Refs #763. Refs #471. Refs #287. Refs #290. Support of running OMSSA searches from Proteios SE updated by option to import results automatically:

1. Class/file action/file/UseSpectrumFileForOMSSASearchExtension.java in client/servlet/ updated to add new button to create search job and import results. The selected button should be identified by the value of new valid parameter VBoolean SearchOMSSA.VOMSSAIMPORTRESULTSFLAG being set to true.

2. Class/file action/omssa/ViewActiveOMSSAParameterSetStorage.java in client/servlet/ updated to extend the form for inspecting/editing parameters when spectrum files have been selected for searching, in which case a new field set "OMSSA - Additional Options not in Parameter Set" will be added, with initially a single check box "Import results", coupled to new valid parameter VBoolean SearchOMSSA.VOMSSAIMPORTRESULTSFLAG. The check box should as default not be checked.

3. Class/file action/omssa/SaveOMSSAParameterSetStorage.java in client/servlet/ updated to retrieve the value of new valid parameter VBoolean SearchOMSSA.VOMSSAIMPORTRESULTSFLAG and add it as parameter to the forward action link, using the same valid parameter. This ensures that the value is transferred to the action creating the search job after the parameters have been saved.

4. Class/file action/omssa/SearchOMSSA.java in client/servlet/ updated to retrieve the value of new valid parameter VBoolean SearchOMSSA.VOMSSAIMPORTRESULTSFLAG and transfer it as job parameter to the created search job.

5. Class/file plugins/SearchOMSSAPlugin.java in plugin/ updated:
   a. Private method void execute(Request request, Response response, ProgressReporter progress) updated to retrieve value of Boolean results import flag from job parameter, and use it as argument when calling updated private method void omssaSearchViaWebInterface(..., Boolean importResultsFlag, Boolean convertMzDataToMgfFlag) or void omssaSearchLocal(..., Boolean importResultsFlag, Boolean convertMzDataToMgfFlag).
   b. Private method void omssaSearchViaWebInterface(...) updated with new argument Boolean importResultsFlag. If the value is true, new private method Job createImportJob(String pluginClassName, String jobName, File inputFile) is called to create an import job to import the results. Job done message updated with info regarding uploaded file and optionally created import job.
   c. Private method void omssaSearchLocal(...) updated with new argument Boolean importResultsFlag. If the value is true, new private method Job createImportJob(String pluginClassName, String jobName, File inputFile) is called to create an import job to import the results. Job done message updated with info regarding uploaded file and optionally created import job.
   d. Private method void uploadFileViaWebInterface(...) updated to File uploadFileViaWebInterface(...) and return the uploaded results file item.
   e. Private method void uploadOMSSAOutputFile(...) updated to File uploadOMSSAOutputFile(...) and return the uploaded results file item.
   f. New private method Job createImportJob(String pluginClassName, String jobName, File inputFile) added. It creates an import job to import results.

6. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

7. Default icon settings file "default" in icons/ in client/servlet/ updated with icon assignments for new string keys.